Selective antisense compounds and uses thereof

ABSTRACT

The present invention provides oligomeric compounds. Certain such oligomeric compounds are useful for hybridizing to a complementary nucleic acid, including but not limited, to nucleic acids in a cell. In certain embodiments, hybridization results in modulation of the amount activity or expression of the target nucleic acid in a cell.

FIELD OF THE INVENTION

The present invention pertains generally to chemically-modified oligonucleotides for use in research, diagnostics, and/or therapeutics.

SEQUENCE LISTING

The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled CORE0099USA2C1SEQ_ST25.txt, created Dec. 17, 2018 which is 300 Kb in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Antisense compounds have been used to modulate target nucleic acids. Antisense compounds comprising a variety of chemical modifications and motifs have been reported. In certain instances, such compounds are useful as research tools, diagnostic reagents, and as therapeutic agents. In certain instances antisense compounds have been shown to modulate protein expression by binding to a target messenger RNA (mRNA) encoding the protein. In certain instances, such binding of an antisense compound to its target mRNA results in cleavage of the mRNA. Antisense compounds that modulate processing of a pre-mRNA have also been reported. Such antisense compounds alter splicing, interfere with polyadenlyation or prevent formation of the 5′-cap of a pre-mRNA.

SUMMARY OF THE INVENTION

In certain embodiments, the present invention provides oligomeric compounds comprising oligonucleotides. In certain embodiments, such oligonucleotides comprise a region having a gapmer motif. In certain embodiments, such oligonucleotides consist of a region having a gapmer motif.

The present disclosure provides the following non-limiting numbered embodiments:

Embodiment 1

A oligomeric compound comprising a modified oligonucleotide consisting of 10 to 30 linked nucleosides, wherein the modified oligonucleotide has a modification motif comprising: a 5′-region consisting of 2-8 linked 5′-region nucleosides, each independently selected from among a modified nucleoside and an unmodified deoxynucleoside, provided that at least one 5′-region nucleoside is a modified nucleoside and wherein the 3′-most 5′-region nucleoside is a modified nucleoside;

-   -   a 3′-region consisting of 2-8 linked 3′-region nucleosides, each         independently selected from among a modified nucleoside and an         unmodified deoxynucleoside, provided that at least one 3′-region         nucleoside is a modified nucleoside and wherein the 5′-most         3′-region nucleoside is a modified nucleoside; and     -   a central region between the 5′-region and the 3′-region         consisting of 6-12 linked central region nucleosides, each         independently selected from among: a modified nucleoside and an         unmodified deoxynucleoside, wherein the 5′-most central region         nucleoside is an unmodified deoxynucleoside and the 3′-most         central region nucleoside is an unmodified deoxynucleoside;     -   wherein the modified oligonucleotide has a nucleobase sequence         complementary to the nucleobase sequence of a target region of a         target nucleic acid.

Embodiment 2

The oligomeric compound of embodiment 1, wherein the nucleobase sequence of the target region of the target nucleic acid differs from the nucleobase sequence of at least one non-target nucleic acid by 1-3 differentiating nucleobases.

Embodiment 3

The oligomeric compound of embodiment 1, the nucleobase sequence of the target region of the target nucleic acid differs from the nucleobase sequence of at least one non-target nucleic acid by a single differentiating nucleobase.

Embodiment 4

The oligomeric compound of embodiment 2 or 3, wherein the target nucleic acid and the non-target nucleic acid are alleles of the same gene.

Embodiment 5

The oligomeric compound of embodiment 4, wherein the single differentiating nucleobase is a single-nucleotide polymorphism.

Embodiment 6

The oligomeric compound of embodiment 5, wherein the single-nucleotide polymorphism is associated with a disease.

Embodiment 7

The oligomeric compound of embodiment 6, wherein the disease is Huntington's disease.

Embodiment 8

The oligomeric compound of embodiment 6, wherein the single-nucleotide polymorphism is selected from among: rs6446723, rs3856973, rs2285086, rs363092, rs916171, rs6844859, rs7691627, rs4690073, rs2024115, rs11731237, rs362296, rs10015979, rs7659144, rs363096, rs362273, rs16843804, rs362271, rs362275, rs3121419, rs362272, rs3775061, rs34315806, rs363099, rs2298967, rs363088, rs363064, rs363102, rs2798235, rs363080, rs363072, rs363125, rs362303, rs362310, rs10488840, rs362325, rs35892913, rs363102, rs363096, rs11731237, rs10015979, rs363080, rs2798235, rs1936032, rs2276881, rs363070, rs35892913, rs12502045, rs6446723, rs7685686, rs3733217, rs6844859, and rs362331.

Embodiment 9

The oligomeric compound of embodiment 8, wherein the single-nucleotide polymorphism is selected from among: rs7685686, rs362303 rs4690072 and rs363088 Embodiment 10: The oligomeric compound of embodiment 2 or 3, wherein the target nucleic acid and the non-target nucleic acid are transcripts from different genes.

Embodiment 11

The oligomeric compound of any of embodiments 1-10, wherein the 3′-most 5′-region nucleoside comprises a bicyclic sugar moiety.

Embodiment 12

The oligomeric compound of embodiment 11, wherein the 3′-most 5′-region nucleoside comprises a cEt sugar moiety.

Embodiment 13

The oligomeric compound of embodiment 11, wherein the 3′-most 5′-region nucleoside comprises an LNA sugar moiety.

Embodiment 14

The oligomeric compound of any of embodiments 1-13, wherein the central region consists of 6-10 linked nucleosides.

Embodiment 15

The oligomeric compound of any of embodiments 1-14, wherein the central region consists of 6-9 linked nucleosides.

Embodiment 16

The oligomeric compound of embodiment 15, wherein the central region consists of 6 linked nucleosides.

Embodiment 17

The oligomeric compound of embodiment 15, wherein the central region consists of 7 linked nucleosides.

Embodiment 18

The oligomeric compound of embodiment 15, wherein the central region consists of 8 linked nucleosides.

Embodiment 19

The oligomeric compound of embodiment 15, wherein the central region consists of 9 linked nucleosides.

Embodiment 20

The oligomeric compound of any of embodiments 1-19, wherein each central region nucleoside is an unmodified deoxynucleoside.

Embodiment 21

The oligomeric compound of any of embodiments 1-19, wherein at least one central region nucleoside is a modified nucleoside.

Embodiment 22

The oligomeric compound of embodiment 21, wherein one central region nucleoside is a modified nucleoside and each of the other central region nucleosides is an unmodified deoxynucleoside.

Embodiment 23

The oligomeric compound of embodiment 21, wherein two central region nucleosides are modified nucleosides and each of the other central region nucleosides is an unmodified deoxynucleoside.

Embodiment 24

The oligomeric compound of any of embodiments 21-23 wherein at least one modified central region nucleoside is an RNA-like nucleoside.

Embodiment 25

The oligomeric compound of any of embodiments 21-23 comprising at least one modified central region nucleoside comprising a modified sugar moiety.

Embodiment 26

The oligomeric compound of any of embodiments 21-25 comprising at least one modified central region nucleoside comprising a 5′-methyl-2′-deoxy sugar moiety.

Embodiment 27

The oligomeric compound of any of embodiments 21-26 comprising at least one modified central region nucleoside comprising a bicyclic sugar moiety.

Embodiment 28

The oligomeric compound of any of embodiments 21-27 comprising at least one modified central region nucleoside comprising a cEt sugar moiety.

Embodiment 29

The oligomeric compound of any of embodiments 21-28 comprising at least one modified central region nucleoside comprising an LNA sugar moiety.

Embodiment 30

The oligomeric compound of any of embodiments 21-29 comprising at least one modified central region nucleoside comprising an α-LNA sugar moiety.

Embodiment 31

The oligomeric compound of any of embodiments 21-29 comprising at least one modified central region nucleoside comprising a 2′-substituted sugar moiety.

Embodiment 32

The oligomeric compound of embodiment 31 wherein at least one modified central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF3, OCF3, O, S, or N(Rm)-alkyl; O, S, or N(Rm)-alkenyl; O, S or N(Rm)-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH2)2SCH3, O—(CH2)2-O—N(Rm)(Rn) or O—CH2-C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl;

-   -   wherein each optionally substituted group is optionally         substituted with a substituent group independently selected from         among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro         (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl,         alkenyl and alkynyl.

Embodiment 33

The oligomeric compound of embodiment 32 wherein at least one modified central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: a halogen, OCH₃, OCH₂F, OCHF₂, OCF₃, OCH₂CH₃, O(CH₂)₂F, OCH₂CHF₂, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)2-OCH₃, O(CH₂)2-SCH₃, O(CH₂)₂—OCF₃, O(CH₂)₃—N(R₁)(R₂), O(CH₂)₂—ON(R₁)(R₂), O(CH₂)₂—O(CH₂)₂—N(R₁)(R₂), OCH₂C(═O)—N(R₁)(R₂), OCH₂C(═O)—N(R₃)—(CH₂)₂—N(R₁)(R₂), and O(CH₂)₂—N(R₃)—C(═NR₄)[N(R₁)(R₂)]; wherein R₁, R₂, R₃ and R₄ are each, independently, H or C₁-C₆ alkyl.

Embodiment 34

The oligomeric compound of embodiment 33 wherein the 2′ substituent is selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃ (MOE), O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 35

The oligomeric compound of any of embodiments 21-34 comprising at least one modified central region nucleoside comprising a 2′-MOE sugar moiety.

Embodiment 36

The oligomeric compound of any of embodiments 21-35 comprising at least one modified central region nucleoside comprising a 2′-OMe sugar moiety.

Embodiment 37

The oligomeric compound of any of embodiments 21-36 comprising at least one modified central region nucleoside comprising a 2′-F sugar moiety.

Embodiment 38

The oligomeric compound of any of embodiments 21-37 comprising at least one modified central region nucleoside comprising a 2′-(ara)-F sugar moiety.

Embodiment 39

The oligomeric compound of any of embodiments 21-38 comprising at least one modified central region nucleoside comprising a sugar surrogate.

Embodiment 40

The oligomeric compound of embodiment 39 comprising at least one modified central region nucleoside comprising an F-HNA sugar moiety.

Embodiment 41

The oligomeric compound of embodiment 39 or 40 comprising at least one modified central region nucleoside comprising an HNA sugar moiety.

Embodiment 42

The oligomeric compound of any of embodiments 21-41 comprising at least one modified central region nucleoside comprising a modified nucleobase.

Embodiment 43

The oligomeric compound of embodiment 42 comprising at least one modified central region nucleoside comprising a modified nucleobase selected from a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 44

The oligomeric compound of any of embodiments 21-43, wherein the 2^(nd) nucleoside from the 5′-end of the central region is a modified nucleoside.

Embodiment 45

The oligomeric compound of any of embodiments 21-44, wherein the 3^(rd) nucleoside from the 5′-end of the central region is a modified nucleoside.

Embodiment 46

The oligomeric compound of any of embodiments 21-45, wherein the 4^(th) nucleoside from the 5′-end of the central region is a modified nucleoside.

Embodiment 47

The oligomeric compound of any of embodiments 21-46, wherein the 5^(th) nucleoside from the 5′-end of the central region is a modified nucleoside.

Embodiment 48

The oligomeric compound of any of embodiments 21-47, wherein the 6^(th) nucleoside from the 5′-end of the central region is a modified nucleoside.

Embodiment 49

The oligomeric compound of any of embodiments 21-48, wherein the 8^(th) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 50

The oligomeric compound of any of embodiments 21-49, wherein the 7^(th) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 51

The oligomeric compound of any of embodiments 21-50, wherein the 6^(th) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 52

The oligomeric compound of any of embodiments 21-51, wherein the 5^(th) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 53

The oligomeric compound of any of embodiments 21-52, wherein the 4^(th) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 54

The oligomeric compound of any of embodiments 21-53, wherein the 3^(rd) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 55

The oligomeric compound of any of embodiments 21-54, wherein the 2^(nd) nucleoside from the 3′-end of the central region is a modified nucleoside.

Embodiment 56

The oligomeric compound of any of embodiments 21-55, wherein the modified nucleoside is a 5′-methyl-2′-deoxy sugar moiety.

Embodiment 57

The oligomeric compound of any of embodiments 21-55, wherein the modified nucleoside is a 2-thio pyrimidine.

Embodiment 58

The oligomeric compound of any of embodiments 21-55, wherein the central region comprises no region having more than 4 contiguous unmodified deoxynucleosides.

Embodiment 59

The oligomeric compound of any of embodiments 21-55, wherein the central region comprises no region having more than 5 contiguous unmodified deoxynucleosides.

Embodiment 60

The oligomeric compound of any of embodiments 21-55, wherein the central region comprises no region having more than 6 contiguous unmodified deoxynucleosides.

Embodiment 61

The oligomeric compound of any of embodiments 21-55, wherein the central region comprises no region having more than 7 contiguous unmodified deoxynucleosides.

Embodiment 62

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDDDDDD, DDDDXDDDDD; DDDDDXDDDDD; DDDXDDDDD; DDDDXDDDDDD; DDDDXDDDD; DDXDDDDDD; DDDXDDDDDD; DXDDDDDD; DDXDDDDDDD; DDXDDDDD; DDXDDDXDDD; DDDXDDDXDDD; DXDDDXDDD; DDXDDDXDD; DDXDDDDXDDD; DDXDDDDXDD; DXDDDDXDDD; DDDDXDDD; DDDXDDD; DXDDDDDDD; DDDDXXDDD; and DXXDXXDXX; wherein

-   -   each D is an unmodified deoxynucleoside; and each X is a         modified nucleoside.

Embodiment 63

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDDDDD; DXDDDDDDD; DDXDDDDDD; DDDXDDDDD; DDDDXDDDD; DDDDDXDDD; DDDDDDXDD; DDDDDDDXD; DXXDDDDDD; DDDDDDXXD; DDXXDDDDD; DDDXXDDDD; DDDDXXDDD; DDDDDXXDD; DXDDDDDXD; DXDDDDXDD; DXDDDXDDD; DXDDXDDDD; DXDXDDDDD; DDXDDDDXD; DDXDDDXDD; DDXDDXDDD; DDXDXDDDD; DDDXDDDXD; DDDXDDXDD; DDDXDXDDD; DDDDXDDXD; DDDDXDXDD; and DDDDDXDXD wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside.

Embodiment 64

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDDDD, DDDDXDDDD, DXDDDDDDD, DXXDDDDDD, DDXDDDDDD, DDDXDDDDD, DDDDXDDDD, DDDDDXDDD, DDDDDDXDD, and DDDDDDDXD.

Embodiment 65

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDDDD, DXDDDDDD, DDXDDDDD, DDDXDDDD, DDDDXDDD, DDDDDXDD, DDDDDDXD, DXDDDDXD, DXDDDXDD, DXDDXDDD, DXDXDDDD, DXXDDDDD, DDXXDDDD, DDXDXDDD, DDXDDXDD, DXDDDDXD, DDDXXDDD, DDDXDXDD, DDDXDDXD, DDDDXXDD, DDDDXDXD, and DDDDDXXD.

Embodiment 66

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDDD, DXDDDDD, DDXDDDD, DDDXDDD, DDDDXDD, DDDDDXD, DXDDDXD, DXDDXDD, DXDXDDD, DXXDDDD, DDXXDDD, DDXDXDD, DDXDDXD, DDDXXDD, DDDXDXD, and DDDDXXD.

Embodiment 67

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDD, DXDDDD, DDXDDD, DDDXDD, DDDDXD, DXXDDD, DXDXDD, DXDDXD, DDXXDD, DDXDXD, and DDDXXD.

Embodiment 68

The oligomeric compound of any of embodiments 1-14 or 21-59, wherein the central region has a nucleoside motif selected from among: DDDDDD, DDDDDDD, DDDDDDDD, DDDDDDDDD, DDDDDDDDDD, DXDDDD, DDXDDD, DDDXDD, DDDDXD, DXDDDDD, DDXDDDD, DDDXDDD, DDDDXDD, DDDDDXD, DXDDDDDD, DDXDDDDD, DDDXDDDD, DDDDXDDD, DDDDDXDD, DDDDDDXD, DXDDDDDDD; DDXDDDDDD, DDDXDDDDD, DDDDXDDDD, DDDDDXDDD, DDDDDDXDD, DDDDDDDXD, DXDDDDDDDD, DDXDDDDDDD, DDDXDDDDDD, DDDDXDDDDD, DDDDDXDDDD, DDDDDDXDDD, DDDDDDDXDD, and DDDDDDDDXD.

Embodiment 69

The oligomeric compound of embodiments 62-68, wherein each X comprises a modified nucleobase.

Embodiment 70

The oligomeric compound of embodiments 62-68, wherein each X comprises a modified sugar moiety.

Embodiment 71

The oligomeric compound of embodiments 62-68, wherein each X comprises 2-thio-thymidine.

Embodiment 72

The oligomeric compound of embodiments 62-68, wherein each X nucleoside comprises an F-HNA sugar moiety.

Embodiment 73

The oligomeric compound of embodiments 62-68, wherein the nucleobase sequence of the target region of the target nucleic acid differs from the nucleobase sequence of at least one non-target nucleic acid by a single differentiating nucleobase, and wherein the location of the single differentiating nucleobase is represented by X.

Embodiment 74

The oligomeric compound of embodiment 73, wherein the target nucleic acid and the non-target nucleic acid are alleles of the same gene.

Embodiment 75

The oligomeric compound of embodiment 73, wherein the single differentiating nucleobase is a single-nucleotide polymorphism.

Embodiment 76

The oligomeric compound of any of embodiments 1-75, wherein the 5′ region consists of 2 linked 5′-region nucleosides.

Embodiment 77

The oligomeric compound of any of embodiments 1-75, wherein the 5′ region consists of 3 linked 5′-region nucleosides.

Embodiment 78

The oligomeric compound of any of embodiments 1-75, wherein the 5′ region consists of 4 linked 5′-region nucleosides.

Embodiment 79

The oligomeric compound of any of embodiments 1-75, wherein the 5′ region consists of 5 linked 5′-region nucleosides.

Embodiment 80

The oligomeric compound of any of embodiments 1-75, wherein the 5′ region consists of 6 linked 5′-region nucleosides.

Embodiment 81

The oligomeric compound of any of embodiments 1-80, wherein at least one 5′-region nucleoside is an unmodified deoxynucleoside.

Embodiment 82

The oligomeric compound of any of embodiments 1-80, wherein each 5′-region nucleoside is a modified nucleoside.

Embodiment 83

The oligomeric compound of any of embodiments 1-80 wherein at least one 5′-region nucleoside is an RNA-like nucleoside.

Embodiment 84

The oligomeric compound of any of embodiments 1-80 wherein each 5′-region nucleoside is an RNA-like nucleoside.

Embodiment 85

The oligomeric compound of any of embodiments 1-80 comprising at least one modified 5′-region nucleoside comprising a modified sugar.

Embodiment 86

The oligomeric compound of embodiment 80 comprising at least one modified 5′-region nucleoside comprising a bicyclic sugar moiety.

Embodiment 87

The oligomeric compound of embodiment 86 comprising at least one modified 5′-region nucleoside comprising a cEt sugar moiety.

Embodiment 88

The oligomeric compound of embodiment 85 or 86 comprising at least one modified 5′-region nucleoside comprising an LNA sugar moiety.

Embodiment 89

The oligomeric compound of any of embodiments 76-80 comprising of at least one modified 5′-region nucleoside comprising a 2′-substituted sugar moiety.

Embodiment 90

The oligomeric compound of embodiment 89 wherein at least one modified central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl;

-   -   wherein each optionally substituted group is optionally         substituted with a substituent group independently selected from         among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro         (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl,         alkenyl and alkynyl.

Embodiment 91

The oligomeric compound of embodiment 90 wherein at least one modified 5′-region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCH₂F, OCHF₂, OCF₃, OCH₂CH₃, O(CH₂)₂F, OCH₂CHF₂, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃ (MOE), O(CH₂)₂—SCH₃, O(CH₂)₂—OCF₃, O(CH₂)₃—N(R₁)(R₂), O(CH₂)₂—ON(R₁)(R₂), O(CH₂)₂—O(CH₂)₂—N(R₁)(R₂), OCH₂C(═O)—N(R₁)(R₂), OCH₂C(═O)—N(R₃)—(CH₂)₂—N(R₁)(R₂), and O(CH₂)₂—N(R₃)—C(═NR₄)[N(R₁)(R₂)]; wherein R₁, R₂, R₃ and R₄ are each, independently, H or C₁-C₆ alkyl.

Embodiment 92

The oligomeric compound of embodiment 91, wherein the 2′-substituent is selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 93

The oligomeric compound of any of embodiments 89-92 comprising at least one modified 5′-region nucleoside comprising a 2′-MOE sugar moiety.

Embodiment 94

The oligomeric compound of any of embodiments 89-92 comprising at least one modified 5′-region nucleoside comprising a 2′-OMe sugar moiety.

Embodiment 95

The oligomeric compound of any of embodiments 89-92 comprising at least one modified 5′-region nucleoside comprising a 2′-F sugar moiety.

Embodiment 96

The oligomeric compound of any of embodiments 89-92 comprising at least one modified 5′-region nucleoside comprising a 2′-(ara)-F sugar moiety.

Embodiment 97

The oligomeric compound of any of embodiments 82-96 comprising of at least one modified 5′-region nucleoside comprising a sugar surrogate.

Embodiment 98

The oligomeric compound of embodiment 97 comprising at least one modified 5′-region nucleoside comprising an F-HNA sugar moiety.

Embodiment 99

The oligomeric compound of embodiment 97 or 98 comprising at least one modified 5′-region nucleoside comprising an HNA sugar moiety.

Embodiment 100

The oligomeric compound of any of embodiments 1-99 comprising at least one modified 5′-region nucleoside comprising a modified nucleobase.

Embodiment 101

The oligomeric compound of embodiment 100, wherein the modified nucleoside comprises 2-thio-thymidine.

Embodiment 102

The oligomeric compound of any of embodiments 1-101, wherein the 5′-region has a motif selected from among:

-   -   ADDA; ABDAA; ABBA; ABB; ABAA; AABAA; AAABAA; AAAABAA; AAAAABAA;         AAABAA; AABAA; ABAB; ABADB; ABADDB; AAABB; AAAAA; ABBDC; ABDDC;         ABBDCC; ABBDDC; ABBDCC; ABBC; AA; AAA; AAAA; AAAAB; AAAAAAA;         AAAAAAAA; ABBB; AB; ABAB; AAAAB; AABBB; AAAAB; and AABBB,     -   wherein each A is a modified nucleoside of a first type, each B         is a modified nucleoside of a second type, each C is a modified         nucleoside of a third type, and each D is an unmodified         deoxynucleoside.

Embodiment 103

The oligomeric compound of any of embodiments 1-101, wherein the 5′-region has a motif selected from among:

-   -   AB, ABB, AAA, BBB, BBBAA, AAB, BAA, BBAA, AABB, AAAB, ABBW,         ABBWW, ABBB, ABBBB, ABAB, ABABAB, ABABBB, ABABAA, AAABB, AAAABB,         AABB, AAAAB, AABBB, ABBBB, BBBBB, AAABW, AAAAA, BBBBAA, and         AAABW wherein each A is a modified nucleoside of a first type,         each B is a modified nucleoside of a second type, and each W is         a modified nucleoside of a third type.

Embodiment 104

The oligomeric compound of any of embodiments 1-101, wherein the 5′-region has a motif selected from among: ABB; ABAA; AABAA; AAABAA; ABAB; ABADB; AAABB; AAAAA; AA; AAA; AAAA; AAAAB; ABBB; AB; and ABAB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of a third type.

Embodiment 105

The oligomeric compound of embodiments 102-104, wherein each A nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 106

The oligomeric compound of embodiment 105 wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; 0, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 107

The oligomeric compound of embodiment 102-106, wherein each A nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 108

The oligomeric compound of embodiment 107, wherein each A nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 109

The oligomeric compound of embodiments 102-106, wherein each A nucleoside comprises a bicyclic sugar moiety.

Embodiment 110

The oligomeric compound of embodiment 109, wherein each A nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 111

The oligomeric compound of any of embodiments 102-110, wherein each A comprises a modified nucleobase.

Embodiment 112

The oligomeric compound of embodiment 111, wherein each A comprises a modified nucleobase selected from among a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 113

The oligomeric compound of embodiment 112, wherein each A comprises 2-thio-thymidine.

Embodiment 114

The oligomeric compound of embodiment 102-106, wherein each A nucleoside comprises an unmodified 2′-deoxyfuranose sugar moiety.

Embodiment 115

The oligomeric compound of embodiment 102-106, wherein each A nucleoside comprises an F-HNA sugar moiety.

Embodiment 116

The oligomeric compound of any of embodiments 102-115, wherein each B nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 117

The oligomeric compound of embodiment 116, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 118

The oligomeric compound of embodiment 117, wherein each B nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 119

The oligomeric compound of embodiment 118, wherein each B nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 120

The oligomeric compound of any of embodiments 102-115, wherein each B nucleoside comprises a bicyclic sugar moiety.

Embodiment 121

The oligomeric compound of embodiment 120, wherein each B nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 122

The oligomeric compound of any of embodiments 102-115, wherein each B comprises a modified nucleobase.

Embodiment 123

The oligomeric compound of embodiment 122, wherein each B comprises a modified nucleobase selected from among a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 124

The oligomeric compound of embodiment 123, wherein each B comprises 2-thio-thymidine.

Embodiment 125

The oligomeric compound of embodiment 102-106, wherein each B nucleoside comprises an unmodified 2′-deoxyfuranose sugar moiety.

Embodiment 126

The oligomeric compound of embodiment 102-115, wherein each B nucleoside comprises an F-HNA sugar moiety.

Embodiment 127

The oligomeric compound of any of embodiments 102-126, wherein each C nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 128

The oligomeric compound of embodiment 127, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH2-C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 129

The oligomeric compound of embodiment 128, wherein each C nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 130

The oligomeric compound of embodiment 129, wherein each C nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 131

The oligomeric compound of any of embodiments 102-126, wherein each C nucleoside comprises a bicyclic sugar moiety.

Embodiment 132

The oligomeric compound of embodiment 131, wherein each C nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 133

The oligomeric compound of any of embodiments 102-126, wherein each C comprises a modified nucleobase.

Embodiment 134

The oligomeric compound of embodiment 133, wherein each C comprises a modified nucleobase selected from among a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 135

The oligomeric compound of embodiment 134, wherein each C comprises 2-thio-thymidine.

Embodiment 136

The oligomeric compound of embodiment 102-126, wherein each C comprises an F-HNA sugar moiety.

Embodiment 137

The oligomeric compound of embodiment 102-126, wherein each C nucleoside comprises an unmodified 2′-deoxyfuranose sugar moiety.

Embodiment 138

The oligomeric compound of any of embodiments 102-138, wherein each W nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 139

The oligomeric compound of embodiment 138, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 140

The oligomeric compound of embodiment 139, wherein each W nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 141

The oligomeric compound of embodiment 139, wherein each W nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 142

The oligomeric compound of any of embodiments 102-137, wherein each W nucleoside comprises a bicyclic sugar moiety.

Embodiment 143

The oligomeric compound of embodiment 142, wherein each W nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 144

The oligomeric compound of any of embodiments 102-137, wherein each W comprises a modified nucleobase.

Embodiment 145

The oligomeric compound of embodiment 144, wherein each W comprises a modified nucleobase selected from among a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 146

The oligomeric compound of embodiment 145, wherein each W comprises 2-thio-thymidine.

Embodiment 147

The oligomeric compound of embodiment 102-137, wherein each W comprises an F-HNA sugar moiety.

Embodiment 148

The oligomeric compound of embodiment 102-137, wherein each W nucleoside comprises an unmodified 2′-deoxyfuranose sugar moiety.

Embodiment 149

The oligomeric compound of any of embodiments 1-148, wherein the 3′ region consists of 2 linked 3′-region nucleosides.

Embodiment 150

The oligomeric compound of any of embodiments 1-148, wherein the 3′ region consists of 3 linked 3′-region nucleosides.

Embodiment 151

The oligomeric compound of any of embodiments 1-148, wherein the 3′ region consists of 4 linked 3′-region nucleosides.

Embodiment 152

The oligomeric compound of any of embodiments 1-148, wherein the 3′ region consists of 5 linked 3′-region nucleosides.

Embodiment 153

The oligomeric compound of any of embodiments 1-148, wherein the 3′ region consists of 6 linked 3′-region nucleosides.

Embodiment 154

The oligomeric compound of any of embodiments 1-153, wherein at least one 3′-region nucleoside is an unmodified deoxynucleoside.

Embodiment 155

The oligomeric compound of any of embodiments 1-154, wherein each 3′-region nucleoside is a modified nucleoside.

Embodiment 156

The oligomeric compound of any of embodiments 1-153, wherein at least one 3′-region nucleoside is an RNA-like nucleoside.

Embodiment 157

The oligomeric compound of any of embodiments 1-154, wherein each 3′-region nucleoside is an RNA-like nucleoside.

Embodiment 158

The oligomeric compound of any of embodiments 1-153, comprising at least one modified 3′-region nucleoside comprising a modified sugar.

Embodiment 159

The oligomeric compound of embodiment 158, comprising at least one modified 3′-region nucleoside comprising a bicyclic sugar moiety.

Embodiment 160

The oligomeric compound of embodiment 159, comprising at least one modified 3′-region nucleoside comprising a cEt sugar moiety.

Embodiment 161

The oligomeric compound of embodiment 159, comprising at least one modified 3′-region nucleoside comprising an LNA sugar moiety.

Embodiment 162

The oligomeric compound of any of embodiments 1-162 comprising of at least one modified 3′-region nucleoside comprising a 2′-substituted sugar moiety.

Embodiment 163

The oligomeric compound of embodiment 162, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH2-C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 164

The oligomeric compound of embodiment 163 wherein at least one modified 3′-region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCH₂F, OCHF₂, OCF₃, OCH₂CH₃, O(CH₂)₂F, OCH₂CHF₂, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃ (MOE), O(CH₂)₂—SCH₃, O(CH₂)₂—OCF₃, O(CH₂)₃—N(R₁)(R₂), O(CH₂)₂—ON(R₁)(R₂), O(CH₂)₂—O(CH₂)₂—N(R₁)(R₂), OCH₂C(═O)—N(R₁)(R₂), OCH₂C(═O)—N(R₃)—(CH₂)₂—N(R₁)(R₂), and O(CH₂)₂—N(R₃)—C(═NR₄)[N(R₁)(R₂)]; wherein R₁, R₂, R₃ and R₄ are each, independently, H or C₁-C₆ alkyl.

Embodiment 165

The oligomeric compound of embodiment 164, wherein the 2′-substituent is selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH2-CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 166

The oligomeric compound of any of embodiments 162-165 comprising at least one modified 3′-region nucleoside comprising a 2′-MOE sugar moiety.

Embodiment 167

The oligomeric compound of any of embodiments 162-166 comprising at least one modified 3′-region nucleoside comprising a 2′-OMe sugar moiety.

Embodiment 168

The oligomeric compound of any of embodiments 162-167 comprising at least one modified 3′-region nucleoside comprising a 2′-F sugar moiety.

Embodiment 169

The oligomeric compound of any of embodiments 162-168 comprising at least one modified 3′-region nucleoside comprising a 2′-(ara)-F sugar moiety.

Embodiment 170

The oligomeric compound of any of embodiments 162-169 comprising of at least one modified 3′-region nucleoside comprising a sugar surrogate.

Embodiment 171

The oligomeric compound of embodiment 170 comprising at least one modified 3′-region nucleoside comprising an F-HNA sugar moiety.

Embodiment 172

The oligomeric compound of embodiment 170 comprising at least one modified 3′-region nucleoside comprising an HNA sugar moiety.

Embodiment 173

The oligomeric compound of any of embodiments 1-172 comprising at least one modified 3′-region nucleoside comprising a modified nucleobase.

Embodiment 174

The oligomeric compound of any of embodiments 1-173, wherein each A comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃, and each B comprises a bicyclic sugar moiety selected from among: LNA and cEt.

Embodiment 175

The oligomeric compound of embodiment 174, wherein each A comprises O(CH₂)₂—OCH₃ and each B comprises cEt.

Embodiment 176

The oligomeric compound of any of embodiments 1-175, wherein the 3′-region has a motif selected from among: ABB, ABAA, AAABAA, AAAAABAA, AABAA, AAAABAA, AAABAA, ABAB, AAAAA, AAABB, AAAAAAAA, AAAAAAA, AAAAAA, AAAAB, AAAA, AAA, AA, AB, ABBB, ABAB, AABBB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type.

Embodiment 177

The oligomeric compound of embodiments 1-175, wherein the 3′-region has a motif selected from among: ABB; AAABAA; AABAA; AAAABAA; AAAAA; AAABB; AAAAAAAA; AAAAAAA; AAAAAA; AAAAB; AB; ABBB; and ABAB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type.

Embodiment 178

The oligomeric compound of embodiments 1-175, wherein the 3′-region has a motif selected from among: BBA, AAB, AAA, BBB, BBAA, AABB, WBBA, WAAB, BBBA, BBBBA, BBBB, BBBBBA, ABBBBB, BBAAA, AABBB, BBBAA, BBBBA, BBBBB, BABA, AAAAA, BBAAAA, AABBBB, BAAAA, and ABBBB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of a first type, a second type, or a third type.

Embodiment 179

The oligomeric compound of embodiments 176-178, wherein each A nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 180

The oligomeric compound of embodiments 176-178, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl;

-   -   wherein each optionally substituted group is optionally         substituted with a substituent group independently selected from         among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro         (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl,         alkenyl and alkynyl.

Embodiment 181

The oligomeric compound of embodiment 180, wherein each A nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 182

The oligomeric compound of embodiment 181, wherein each A nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 183

The oligomeric compound of embodiments 176-178, wherein each A nucleoside comprises a bicyclic sugar moiety.

Embodiment 184

The oligomeric compound of embodiment 183, wherein each A nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 185

The oligomeric compound of any of embodiments 176-178, wherein each B nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 186

The oligomeric compound of embodiment 185, wherein at least one modified central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl;

-   -   wherein each optionally substituted group is optionally         substituted with a substituent group independently selected from         among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro         (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl,         alkenyl and alkynyl.

Embodiment 187

The oligomeric compound of embodiment 185, wherein each B nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 188

The oligomeric compound of embodiment 187, wherein each B nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 189

The oligomeric compound of any of embodiments 176-178, wherein each B nucleoside comprises a bicyclic sugar moiety.

Embodiment 190

The oligomeric compound of embodiment 189, wherein each B nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 191

The oligomeric compound of any of embodiments 176-190, wherein each A comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃, and each B comprises a bicyclic sugar moiety selected from among: LNA and cEt.

Embodiment 192

The oligomeric compound of embodiment 191, wherein each A comprises O(CH₂)₂—OCH₃ and each B comprises cEt.

Embodiment 193

The oligomeric compound of any of embodiments 176-192, wherein each W nucleoside comprises a 2′-substituted sugar moiety.

Embodiment 194

The oligomeric compound of embodiment 193, wherein at least one central region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH2-C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

Embodiment 195

The oligomeric compound of embodiment 193, wherein each W nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.

Embodiment 196

The oligomeric compound of embodiment 195, wherein each W nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: F, OCH₃, O(CH₂)₂—OCH₃.

Embodiment 197

The oligomeric compound of any of embodiments 176-192, wherein each W nucleoside comprises a bicyclic sugar moiety.

Embodiment 198

The oligomeric compound of embodiment 197, wherein each W nucleoside comprises a bicyclic sugar moiety selected from among: cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA.

Embodiment 199

The oligomeric compound of any of embodiments 176-192, wherein each W comprises a modified nucleobase.

Embodiment 200

The oligomeric compound of embodiment 199, wherein each W comprises a modified nucleobase selected from among a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 201

The oligomeric compound of embodiment 200, wherein each W comprises 2-thio-thymidine.

Embodiment 202

The oligomeric compound of embodiment 176-192, wherein each W comprises an F-HNA sugar moiety.

Embodiment 203

The oligomeric compound of embodiment 202, wherein each W nucleoside comprises an unmodified 2′-deoxyfuranose sugar moiety.

Embodiment 204

The oligomeric compound of embodiments 1-203, wherein the 5′-region has a motif selected from among: AB, ABB, AAA, BBB, BBBAA, AAB, BAA, BBAA, AABB, AAAB, ABBW, ABBWW, ABBB, ABBBB, ABAB, ABABAB, ABABBB, ABABAA, AAABB, AAAABB, AABB, AAAAB, AABBB, ABBBB, BBBBB, AAABW, AAAAA, and BBBBAA;

-   -   wherein the 3′-region has a motif selected from among: BBA, AAB,         AAA, BBB, BBAA, AABB, WBBA, WAAB, BBBA, BBBBA, BBBB, BBBBBA,         ABBBBB, BBAAA, AABBB, BBBAA, BBBBA, BBBBB, BABA, AAAAA, BBAAAA,         AABBBB, BAAAA, and ABBBB;     -   wherein the central region has a nucleoside motif selected from         among: DDDDDD, DDDDDDD, DDDDDDDD, DDDDDDDDD, DDDDDDDDDD,         DXDDDDDDD, DDXDDDDDD, DDDXDDDDD, DDDDXDDDD, DDDDDXDDD,         DDDDDDXDD, DDDDDDDXD, DXXDDDDDD, DDDDDDXXD, DDXXDDDDD,         DDDXXDDDD, DDDDXXDDD, DDDDDXXDD, DXDDDDDXD, DXDDDDXDD,         DXDDDXDDD, DXDDXDDDD, DXDXDDDDD, DDXDDDDXD, DDXDDDXDD,         DDXDDXDDD, DDXDXDDDD, DDDXDDDXD, DDDXDDXDD, DDDXDXDDD,         DDDDXDDXD, DDDDXDXDD, and DDDDDXDXD, DDDDDDDD, DXDDDDDD,         DDXDDDDD, DDDXDDDD, DDDDXDDD, DDDDDXDD, DDDDDDXD, DXDDDDXD,         DXDDDXDD, DXDDXDDD, DXDXDDDD, DXXDDDDD, DDXXDDDD, DDXDXDDD,         DDXDDXDD, DXDDDDXD, DDDXXDDD, DDDXDXDD, DDDXDDXD, DDDDXXDD,         DDDDXDXD, and DDDDDXXD, DXDDDDD, DDXDDDD, DDDXDDD, DDDDXDD,         DDDDDXD, DXDDDXD, DXDDXDD, DXDXDDD, DXXDDDD, DDXXDDD, DDXDXDD,         DDXDDXD, DDDXXDD, DDDXDXD, and DDDDXXD, DXDDDD, DDXDDD, DDDXDD,         DDDDXD, DXXDDD, DXDXDD, DXDDXD, DDXXDD, DDXDXD, and DDDXXD; and     -   wherein each A is a modified nucleoside of a first type, each B         is a modified nucleoside of a second type, each W is a modified         nucleoside of a first type, a second type, or a third type, each         D is an unmodified deoxynucleoside, and each X is a modified         nucleoside or a modified nucleobase.

Embodiment 205

The oligomeric compound of embodiment 204, wherein the 5′-region has a motif selected from among: AB, ABB, AAA, BBB, BBBAA, AAB, BAA, BBAA, AABB, ABBW, ABBWW, ABBB, ABBBB, ABAB, ABABAB, ABABBB, ABABAA, AAABB, AAAABB, AABB, AAAAB, AABBB, ABBBB, BBBBB, AAABW, and BBBBAA; and wherein the 3′-region has a BBA motif.

Embodiment 206

The oligomeric compound of embodiment 204 or 205, wherein one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

Embodiment 207

The oligomeric compound of embodiment 204 or 205, wherein one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises FHNA.

Embodiment 208

The oligomeric compound of embodiment 204 or 205, wherein one of A or B comprises cEt, another of A or B comprises a 2′-modified sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

Embodiment 209

The oligomeric compound of embodiment 204 or 205, wherein one of A or B comprises cEt, another of A or B comprises a 2′-modified sugar moiety, and W comprises FHNA.

Embodiment 210

The oligomeric compound of embodiment 204 or 205, wherein each A comprises MOE, each B comprises cEt, and each W is selected from among cEt or FHNA.

Embodiment 211

The oligomeric compound of embodiment 204 or 205, wherein each W comprises cEt.

Embodiment 212

The oligomeric compound of embodiment 204 or 205, wherein each W comprises 2-thio-thymidine.

Embodiment 213

The oligomeric compound of embodiment 204 or 205, wherein each W comprises FHNA.

Embodiment 214

The oligomeric compound of any of embodiments 1-213 comprising at least one modified internucleoside linkage.

Embodiment 215

The oligomeric compound of embodiment 214, wherein each internucleoside linkage is a modified internucleoside linkage.

Embodiment 216

The oligomeric compound of embodiment 214 or 215 comprising at least one phosphorothioate internucleoside linkage.

Embodiment 217

The oligomeric compound of any of embodiments 214 or 215 comprising at least one methylphosphonate internucleoside linkage.

Embodiment 218

The oligomeric compound of any of embodiments 214 or 215 comprising one methylphosphonate internucleoside linkage.

Embodiment 219

The oligomeric compound of any of embodiments 214 or 215 comprising two methylphosphonate internucleoside linkages.

Embodiment 220

The oligomeric compound of embodiment 217, wherein at least one of the 3^(rd), 4^(th)5^(th), 6^(th) and/or 7^(th) internucleoside from the 5′-end is a methylphosphonate internucleoside linkage.

Embodiment 221

The oligomeric compound of embodiment 217, wherein at least one of the 3^(rd), 4^(th), 5^(th), 6^(th) and/or 7^(th) internucleoside from the 3′-end is a methylphosphonate internucleoside linkage.

Embodiment 222

The oligomeric compound of embodiment 217, wherein at least one of the 3^(rd), 4^(th) 5^(th), 6^(th), 7^(th), 8^(th), 9^(th), 10^(th), 11^(th), and/or 12^(th) internucleoside from the 5′-end is a methylphosphonate internucleoside linkage, and wherein at least one of the 3^(rd), 4^(th), 5^(th), 6^(th), 7^(th), 8^(th), 9^(th), 10^(th), 11^(th), and/or 12^(th) internucleoside from the 5′-end is a modified nucleoside.

Embodiment 223

The oligomeric compound of embodiment 217, wherein at least one of the 3^(rd), 4^(th), 5^(th), 6^(th), 7^(th), 8^(th), 9^(th), 10^(th), 11^(th), and/or 12^(th) internucleoside from the 3′-end is a methylphosphonate internucleoside linkage, and wherein at least one of the 3^(rd), 4^(th), 5^(th), 6^(th), 7^(th), 8^(th), 9^(th), 10^(th), 11^(th), and/or 12^(th) internucleoside from the 3′-end is a modified nucleoside.

Embodiment 224

The oligomeric compound of any of embodiments 1-223 comprising at least one conjugate group.

Embodiment 225

The oligomeric compound of embodiment 1-223, wherein the conjugate group consists of a conjugate.

Embodiment 226

The oligomeric compound of embodiment 225, wherein the conjugate group consists of a conjugate and a conjugate linker.

Embodiment 227

The oligomeric compound of any of embodiments 1-226, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 228

The oligomeric compound of any of embodiments 1-226, wherein the nucleobase sequence of the modified oligonucleotide contains one mismatch relative to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 229

The oligomeric compound of any of embodiments 1-226, wherein the nucleobase sequence of the modified oligonucleotide contains two mismatches relative to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 230

The oligomeric compound of any of embodiments 1-226, wherein the nucleobase sequence of the modified oligonucleotide comprises a hybridizing region and at least one non-targeting region, wherein the nucleobase sequence of the hybridizing region is complementary to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 231

The oligomeric compound of embodiment 230, wherein the nucleobase sequence of the hybridizing region is 100% complementary to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 232

The oligomeric compound of embodiment 230, wherein the nucleobase sequence of the hybridizing region contains one mismatche relative to the nucleobase sequence of the target region of the target nucleic acid.

Embodiment 233

The oligomeric compound of any of embodiments 230-232, wherein the nucleobase sequence of at least one non-targeting region is complementary to a portion of the hybridizing region of the modified oligonucleotide.

Embodiment 234

The oligomeric compound of embodiment 233, wherein the nucleobase sequence of at least one non-targeting region is 100% complementary to a portion of the hybridizing region of the modified oligonucleotide.

Embodiment 235

The oligomeric compound of embodiment 1-234 wherein the nucleobase sequence of the modified oligonucleotide comprises two non-targeting regions flanking a central hybridizing region.

Embodiment 236

The oligomeric compound of embodiment 235, wherein the two non-targeting regions are complementary to one another.

Embodiment 237

The oligomeric compound of embodiment 236, wherein the two non-targeting regions are 100% complementary to one another.

Embodiment 238

The oligomeric compound of any of embodiments 2-237, wherein the nucleobase sequence of the modified oligonucleotide aligns with the nucleobase of the target region of the target nucleic acid such that a distinguishing nucleobase of the target region of the target nucleic acid aligns with a target-selective nucleoside within the central region of the modified oligonucleotide.

Embodiment 239

The oligomeric compound of any of embodiments 3-237, wherein the nucleobase sequence of the modified oligonucleotide aligns with the nucleobase of the target region of the target nucleic acid such that the single distinguishing nucleobase of the target region of the target nucleic acid aligns with a target-selective nucleoside within the central region of the modified oligonucleotide.

Embodiment 240

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is the 5′-most nucleoside of the central region.

Embodiment 241

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is the 2^(nd) nucleoside from the 5′-end of the central region.

Embodiment 242

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is at the 3^(rd) nucleoside from the 5′-end of the central region.

Embodiment 243

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is at the 5^(t) nucleoside from the 5′-end of the central region.

Embodiment 244

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is at the 7^(t) nucleoside from the 5′-end of the central region.

Embodiment 245

The oligomeric compound of embodiment 238 or 239, wherein the target-selective nucleoside is at the 9^(t) nucleoside from the 5′-end of the central region.

Embodiment 246

The oligomeric compound of any of embodiments 238 or 239, or 241-245, wherein the target-selective nucleoside is at the 2^(nd) nucleoside from the 3′-end of the central region.

Embodiment 247

The oligomeric compound of any of embodiments 238 or 239, or 241-245, wherein the target-selective nucleoside is at the 5^(th) nucleoside from the 3′-end of the central region.

Embodiment 248

The oligomeric compound of any of embodiments 1-247, wherein target-selective nucleoside is an unmodified deoxynucleoside.

Embodiment 249

The oligomeric compound of any of embodiments 1-247, wherein target-selective nucleoside is a modified nucleoside.

Embodiment 250

The oligomeric compound of embodiment 249, wherein the target-selective nucleoside is a sugar modified nucleoside.

Embodiment 251

The oligomeric compound of embodiment 250, wherein the target-selective nucleoside comprises a sugar modification selected from among: 2′-MOE, 2′-F, 2′-(ara)-F, HNA, FHNA, cEt, and α-L-LNA.

Embodiment 252

The oligomeric compound of any of embodiments 1-251, wherein the target-selective nucleoside comprises a nucleobase modification.

Embodiment 253

The oligomeric compound of embodiment 252, wherein the modified nucleobase is selected from among: a 2-thio pyrimidine and a 5-propyne pyrimidine.

Embodiment 254

The oligomeric compound of any of embodiments 1-253, wherein the oligomeric compound is an antisense compound.

Embodiment 255

The oligomeric compound of embodiment 254, wherein the oligomeric compound selectively reduces expression of the target relative to the non-target.

Embodiment 256

The oligomeric compound of embodiment 255, wherein the oligomeric compound reduces expression of target at least two-fold more than it reduces expression of the non-target.

Embodiment 257

The oligomeric compound of embodiment 256, having an EC₅₀ for reduction of expression of target that is at least two-fold lower than its EC₅₀ for reduction of expression of the non-target, when measured in cells.

Embodiment 258

The oligomeric compound of embodiment 256, having an ED₅₀ for reduction of expression of target that is at least two-fold lower than its ED₅₀ for reduction of expression of the non-target, when measured in an animal.

Embodiment 259

The oligomeric compound of embodiments 1-10, having an E-E-E-K-K-(D)₇-E-E-K motif, wherein each E is a 2′-MOE nucleoside and each K is a cEt nucleoside.

Embodiment 260

A method comprising contacting a cell with an oligomeric compound of any of embodiments 1-259.

Embodiment 261

The method of embodiment 260, wherein the cell is in vitro.

Embodiment 262

The method of embodiment 260, wherein the cell is in an animal.

Embodiment 263

The method of embodiment 262, wherein the animal is a human.

Embodiment 264

The method of embodiment 263, wherein the animal is a mouse.

Embodiment 265

A pharmaceutical composition comprising an oligomeric compound of any of embodiments 1-259 and a pharmaceutically acceptable carrier or diluent.

Embodiment 266

A method of administering a pharmaceutical composition of embodiment 265 to an animal.

Embodiment 267

The method of embodiment 266, wherein the animal is a human.

Embodiment 268

The method of embodiment 266, wherein the animal is a mouse.

Embodiment 269

Use of an oligomeric compound of any of embodiments 1-259 for the preparation of a medicament for the treatment or amelioration of Huntington's disease.

Embodiment 270

A method of ameliorating a symptom of Huntington's disease, comprising administering an oligomeric compound of any of embodiments 1-259 to an animal in need thereof.

Embodiment 271

The method of embodiment 270, wherein the animal is a human.

Embodiment 272

The method of embodiment 270, wherein the animal is a mouse.

In certain embodiments, including but not limited to any of the above numbered embodiments, oligomeric compounds including oligonucleotides described herein are capable of modulating expression of a target RNA. In certain embodiments, the target RNA is associated with a disease or disorder, or encodes a protein that is associated with a disease or disorder. In certain embodiments, the oligomeric compounds or oligonucleotides provided herein modulate the expression of function of such RNA to alleviate one or more symptom of the disease or disorder.

In certain embodiments, oligomeric compounds including oligonucleotides describe herein are useful in vitro. In certain embodiments such oligomeric compounds are used in diagnostics and/or for target validation experiments.

DETAILED DESCRIPTION OF THE INVENTION

It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention, as claimed. Herein, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including” as well as other forms, such as “includes” and “included”, is not limiting. Also, terms such as “element” or “component” encompass both elements and components comprising one unit and elements and components that comprise more than one subunit, unless specifically stated otherwise.

The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated by reference in their entirety for any purpose.

A. Definitions

Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Certain such techniques and procedures may be found for example in “Carbohydrate Modifications in Antisense Research” Edited by Sangvi and Cook, American Chemical Society, Washington D.C., 1994; “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., 21^(st) edition, 2005; and “Antisense Drug Technology, Principles, Strategies, and Applications” Edited by Stanley T. Crooke, CRC Press, Boca Raton, Fla.; and Sambrook et al., “Molecular Cloning, A laboratory Manual,” 2nd Edition, Cold Spring Harbor Laboratory Press, 1989, which are hereby incorporated by reference for any purpose. Where permitted, all patents, applications, published applications and other publications and other data referred to throughout in the disclosure are incorporated by reference herein in their entirety.

Unless otherwise indicated, the following terms have the following meanings: As used herein, “nucleoside” means a compound comprising a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety.

As used herein, “chemical modification” means a chemical difference in a compound when compared to a naturally occurring counterpart. Chemical modifications of oligonucleotides include nucleoside modifications (including sugar moiety modifications and nucleobase modifications) and internucleoside linkage modifications. In reference to an oligonucleotide, chemical modification does not include differences only in nucleobase sequence.

As used herein, “furanosyl” means a structure comprising a 5-membered ring comprising four carbon atoms and one oxygen atom.

As used herein, “naturally occurring sugar moiety” means a ribofuranosyl as found in naturally occurring RNA or a deoxyribofuranosyl as found in naturally occurring DNA.

As used herein, “sugar moiety” means a naturally occurring sugar moiety or a modified sugar moiety of a nucleoside.

As used herein, “modified sugar moiety” means a substituted sugar moiety or a sugar surrogate.

As used herein, “substituted sugar moiety” means a furanosyl that is not a naturally occurring sugar moiety. Substituted sugar moieties include, but are not limited to furanosyls comprising substituents at the 2′-position, the 3′-position, the 5′-position and/or the 4′-position. Certain substituted sugar moieties are bicyclic sugar moieties.

As used herein, “2′-substituted sugar moiety” means a furanosyl comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2′-substituent of a 2′-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring.

As used herein, “MOE” means —OCH₂CH₂OCH₃.

As used herein, “2′-F nucleoside” refers to a nucleoside comprising a sugar comprising fluoroine at the 2′ position. Unless otherwise indicated, the fluorine in a 2′-F nucleoside is in the ribo position (replacing the OH of a natural ribose).

As used herein, “2′-(ara)-F” refers to a 2′-F substituted nucleoside, wherein the fluoro group is in the arabino position.

As used herein the term “sugar surrogate” means a structure that does not comprise a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside sub-units are capable of linking together and/or linking to other nucleosides to form an oligomeric compound which is capable of hybridizing to a complementary oligomeric compound. Such structures include rings comprising a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g., carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen. Such structures may also comprise substitutions corresponding to those described for substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally comprising additional substituents). Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid). Sugar surrogates include without limitation morpholinos, cyclohexenyls and cyclohexitols.

As used herein, “bicyclic sugar moiety” means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2′-carbon and the 4′-carbon of the furanosyl.

As used herein, “nucleotide” means a nucleoside further comprising a phosphate linking group. As used herein, “linked nucleosides” may or may not be linked by phosphate linkages and thus includes, but is not limited to “linked nucleotides.” As used herein, “linked nucleosides” are nucleosides that are connected in a continuous sequence (i.e. no additional nucleosides are present between those that are linked).

As used herein, “nucleobase” means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and wherein the group of atoms is capable of bonding with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid.

Nucleobases may be naturally occurring or may be modified.

As used herein the terms, “unmodified nucleobase” or “naturally occurring nucleobase” means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U).

As used herein, “modified nucleobase” means any nucleobase that is not a naturally occurring nucleobase.

As used herein, “modified nucleoside” means a nucleoside comprising at least one chemical modification compared to naturally occurring RNA or DNA nucleosides. Modified nucleosides comprise a modified sugar moiety and/or a modified nucleobase.

As used herein, “bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety.

As used herein, “constrained ethyl nucleoside” or “cEt” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH(CH₃)—O-2′bridge.

As used herein, “locked nucleic acid nucleoside” or “LNA” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH₂—O-2′bridge.

As used herein, “2′-substituted nucleoside” means a nucleoside comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted nucleoside is not a bicyclic nucleoside.

As used herein, “2′-deoxynucleoside” means a nucleoside comprising 2′-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (e.g., uracil).

As used herein, “RNA-like nucleoside” means a modified nucleoside that adopts a northern configuration and functions like RNA when incorporated into an oligonucleotide. RNA-like nucleosides include, but are not limited to 3′-endo furanosyl nucleosides and RNA surrogates.

As used herein, “3′-endo-furanosyl nucleoside” means an RNA-like nucleoside that comprises a substituted sugar moiety that has a 3′-endo conformation. 3′-endo-furanosyl nucleosides include, but are not limitied to: 2′-MOE, 2′-F, 2′-OMe, LNA, ENA, and cEt nucleosides.

As used herein, “RNA-surrogate nucleoside” means an RNA-like nucleoside that does not comprise a furanosyl. RNA-surrogate nucleosides include, but are not limited to hexitols and cyclopentanes.

As used herein, “oligonucleotide” means a compound comprising a plurality of linked nucleosides.

In certain embodiments, an oligonucleotide comprises one or more unmodified ribonucleosides (RNA) and/or unmodified deoxyribonucleosides (DNA) and/or one or more modified nucleosides.

As used herein “oligonucleoside” means an oligonucleotide in which none of the internucleoside linkages contains a phosphorus atom. As used herein, oligonucleotides include oligonucleosides.

As used herein, “modified oligonucleotide” means an oligonucleotide comprising at least one modified nucleoside and/or at least one modified internucleoside linkage.

As used herein “internucleoside linkage” means a covalent linkage between adjacent nucleosides in an oligonucleotide.

As used herein “naturally occurring internucleoside linkage” means a 3′ to 5′ phosphodiester linkage.

As used herein, “modified internucleoside linkage” means any internucleoside linkage other than a naturally occurring internucleoside linkage.

As used herein, “oligomeric compound” means a polymeric structure comprising two or more sub-structures. In certain embodiments, an oligomeric compound comprises an oligonucleotide. In certain embodiments, an oligomeric compound comprises one or more conjugate groups and/or terminal groups. In certain embodiments, an oligomeric compound consists of an oligonucleotide.

As used herein, “terminal group” means one or more atom attached to either, or both, the 3′ end or the 5′ end of an oligonucleotide. In certain embodiments a terminal group is a conjugate group. In certain embodiments, a terminal group comprises one or more terminal group nucleosides.

As used herein, “conjugate” means an atom or group of atoms bound to an oligonucleotide or oligomeric compound. In general, conjugate groups modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and/or clearance properties.

As used herein, “conjugate linking group” means any atom or group of atoms used to attach a conjugate to an oligonucleotide or oligomeric compound.

As used herein, “antisense compound” means a compound comprising or consisting of an oligonucleotide at least a portion of which is complementary to a target nucleic acid to which it is capable of hybridizing, resulting in at least one antisense activity.

As used herein, “antisense activity” means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid.

As used herein, “detecting” or “measuring” means that a test or assay for detecting or measuring is performed. Such detection and/or measuring may result in a value of zero. Thus, if a test for detection or measuring results in a finding of no activity (activity of zero), the step of detecting or measuring the activity has nevertheless been performed.

As used herein, “detectable and/or measureable activity” means a measurable activity that is not zero.

As used herein, “essentially unchanged” means little or no change in a particular parameter, particularly relative to another parameter which changes much more. In certain embodiments, a parameter is essentially unchanged when it changes less than 5%. In certain embodiments, a parameter is essentially unchanged if it changes less than two-fold while another parameter changes at least ten-fold. For example, in certain embodiments, an antisense activity is a change in the amount of a target nucleic acid. In certain such embodiments, the amount of a non-target nucleic acid is essentially unchanged if it changes much less than the target nucleic acid does, but the change need not be zero.

As used herein, “expression” means the process by which a gene ultimately results in a protein.

Expression includes, but is not limited to, transcription, post-transcriptional modification (e.g., splicing, polyadenlyation, addition of 5′-cap), and translation.

As used herein, “target nucleic acid” means a nucleic acid molecule to which an antisense compound is intended to hybridize.

As used herein, “non-target nucleic acid” means a nucleic acid molecule to which hybridization of an antisense compound is not intended or desired. In certain embodiments, antisense compounds do hybridize to a non-target, due to homology between the target (intended) and non-target (un-intended).

As used herein, “mRNA” means an RNA molecule that encodes a protein.

As used herein, “pre-mRNA” means an RNA transcript that has not been fully processed into mRNA.

Pre-RNA includes one or more intron.

As used herein, “object RNA” means an RNA molecule other than a target RNA, the amount, activity, splicing, and/or function of which is modulated, either directly or indirectly, by a target nucleic acid.

In certain embodiments, a target nucleic acid modulates splicing of an object RNA. In certain such embodiments, an antisense compound modulates the amount or activity of the target nucleic acid, resulting in a change in the splicing of an object RNA and ultimately resulting in a change in the activity or function of the object RNA.

As used herein, “microRNA” means a naturally occurring, small, non-coding RNA that represses gene expression of at least one mRNA. In certain embodiments, a microRNA represses gene expression by binding to a target site within a 3′ untranslated region of an mRNA. In certain embodiments, a microRNA has a nucleobase sequence as set forth in miRBase, a database of published microRNA sequences found at http://microrna.sanger.ac.uk/sequences/. In certain embodiments, a microRNA has a nucleobase sequence as set forth in miRBase version 12.0 released September 2008, which is herein incorporated by reference in its entirety.

As used herein, “microRNA mimic” means an oligomeric compound having a sequence that is at least partially identical to that of a microRNA. In certain embodiments, a microRNA mimic comprises the microRNA seed region of a microRNA. In certain embodiments, a microRNA mimic modulates translation of more than one target nucleic acids. In certain embodiments, a microRNA mimic is double-stranded.

As used herein, “differentiating nucleobase” means a nucleobase that differs between two nucleic acids. In certain instances, a target region of a target nucleic acid differs by 1-4 nucleobases from a non-target nucleic acid. Each of those differences is refered to as a differentiating nucleobase. In certain instances, a differentiating nucleobase is a single-nucleotide polymorphism.

As used herein, “target-selective nucleoside” means a nucleoside of an antisense compound that corresponds to a differentiating nucleobase of a target nucleic acid.

As used herein, “allele” means one of a pair of copies of a gene existing at a particular locus or marker on a specific chromosome, or one member of a pair of nucleobases existing at a particular locus or marker on a specific chromosome, or one member of a pair of nucleobase sequences existing at a particular locus or marker on a specific chromosome. For a diploid organism or cell or for autosomal chromosomes, each allelic pair will normally occupy corresponding positions (loci) on a pair of homologous chromosomes, one inherited from the mother and one inherited from the father. If these alleles are identical, the organism or cell is said to be “homozygous” for that allele; if they differ, the organism or cell is said to be “heterozygous” for that allele. “Wild-type allele” refers to the genotype typically not associated with disease or dysfunction of the gene product. “Mutant allele” refers to the genotype associated with disease or dysfunction of the gene product.

As used herein, “allelic variant” means a particular identity of an allele, where more than one identity occurs. For example, an allelic variant may refer to either the mutant allele or the wild-type allele.

As used herein, “single nucleotide polymorphism” or “SNP” means a single nucleotide variation between the genomes of individuals of the same species. In some cases, a SNP may be a single nucleotide deletion or insertion. In general, SNPs occur relatively frequently in genomes and thus contribute to genetic diversity. The location of a SNP is generally flanked by highly conserved sequences. An individual may be homozygous or heterozygous for an allele at each SNP site.

As used herein, “single nucleotide polymorphism site” or “SNP site” refers to the nucleotides surrounding a SNP contained in a target nucleic acid to which an antisense compound is targeted.

As used herein, “targeting” or “targeted to” means the association of an antisense compound to a particular target nucleic acid molecule or a particular region of a target nucleic acid molecule. An antisense compound targets a target nucleic acid if it is sufficiently complementary to the target nucleic acid to allow hybridization under physiological conditions.

As used herein, “nucleobase complementarity” or “complementarity” when in reference to nucleobases means a nucleobase that is capable of base pairing with another nucleobase. For example, in DNA, adenine (A) is complementary to thymine (T). For example, in RNA, adenine (A) is complementary to uracil (U). In certain embodiments, complementary nucleobase means a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid. For example, if a nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid, then the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be complementary at that nucleobase pair.

Nucleobases comprising certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.

As used herein, “non-complementary” in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.

As used herein, “complementary” in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides, or nucleic acids) means the capacity of such oligomeric compounds or regions thereof to hybridize to another oligomeric compound or region thereof through nucleobase complementarity under stringent conditions. Complementary oligomeric compounds need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated. In certain embodiments, complementary oligomeric compounds or regions are complementary at 70% of the nucleobases (70% complementary). In certain embodiments, complementary oligomeric compounds or regions are 80% complementary. In certain embodiments, complementary oligomeric compounds or regions are 90% complementary. In certain embodiments, complementary oligomeric compounds or regions are 95% complementary. In certain embodiments, complementary oligomeric compounds or regions are 100% complementary.

As used herein, “mismatch” means a nucleobase of a first oligomeric compound that is not capable of pairing with a nucleobase at a corresponding position of a second oligomeric compound, when the first and second oligomeric compound are aligned. Either or both of the first and second oligomeric compounds may be oligonucleotides.

As used herein, “hybridization” means the pairing of complementary oligomeric compounds (e.g., an antisense compound and its target nucleic acid). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.

As used herein, “specifically hybridizes” means the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site. In certain embodiments, an antisense oligonucleotide specifically hybridizes to more than one target site.

As used herein, “fully complementary” in reference to an oligonucleotide or portion thereof means that each nucleobase of the oligonucleotide or portion thereof is capable of pairing with a nucleobase of a complementary nucleic acid or contiguous portion thereof. Thus, a fully complementary region comprises no mismatches or unhybridized nucleobases in either strand.

As used herein, “percent complementarity” means the percentage of nucleobases of an oligomeric compound that are complementary to an equal-length portion of a target nucleic acid. Percent complementarity is calculated by dividing the number of nucleobases of the oligomeric compound that are complementary to nucleobases at corresponding positions in the target nucleic acid by the total length of the oligomeric compound.

As used herein, “percent identity” means the number ofnucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.

As used herein, “modulation” means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation. For example, modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression. As a further example, modulation of expression can include a change in splice site selection of pre-mRNA processing, resulting in a change in the absolute or relative amount of a particular splice-variant compared to the amount in the absence of modulation.

As used herein, “modification motif” means a pattern of chemical modifications in an oligomeric compound or a region thereof. Motifs may be defined by modifications at certain nucleosides and/or at certain linking groups of an oligomeric compound.

As used herein, “nucleoside motif” means a pattern of nucleoside modifications in an oligomeric compound or a region thereof. The linkages of such an oligomeric compound may be modified or unmodified. Unless otherwise indicated, motifs herein describing only nucleosides are intended to be nucleoside motifs. Thus, in such instances, the linkages are not limited.

As used herein, “sugar motif” means a pattern of sugar modifications in an oligomeric compound or a region thereof.

As used herein, “linkage motif” means a pattern of linkage modifications in an oligomeric compound or region thereof. The nucleosides of such an oligomeric compound may be modified or unmodified. Unless otherwise indicated, motifs herein describing only linkages are intended to be linkage motifs. Thus, in such instances, the nucleosides are not limited.

As used herein, “nucleobase modification motif” means a pattern of modifications to nucleobases along an oligonucleotide. Unless otherwise indicated, a nucleobase modification motif is independent of the nucleobase sequence.

As used herein, “sequence motif” means a pattern of nucleobases arranged along an oligonucleotide or portion thereof. Unless otherwise indicated, a sequence motif is independent of chemical modifications and thus may have any combination of chemical modifications, including no chemical modifications.

As used herein, “type of modification” in reference to a nucleoside or a nucleoside of a “type” means the chemical modification of a nucleoside and includes modified and unmodified nucleosides. Accordingly, unless otherwise indicated, a “nucleoside having a modification of a first type” may be an unmodified nucleoside.

As used herein, “differently modified” mean chemical modifications or chemical substituents that are different from one another, including absence of modifications. Thus, for example, a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified.

Likewise, DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified. For example, a nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.

As used herein, “the same type of modifications” refers to modifications that are the same as one another, including absence of modifications. Thus, for example, two unmodified DNA nucleoside have “the same type of modification,” even though the DNA nucleoside is unmodified. Such nucleosides having the same type modification may comprise different nucleobases.

As used herein, “pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to an animal. In certain embodiments, a pharmaceutically acceptable carrier or diluent is sterile saline. In certain embodiments, such sterile saline is pharmaceutical grade saline.

As used herein, “substituent” and “substituent group,” means an atom or group that replaces the atom or group of a named parent compound. For example a substituent of a modified nucleoside is any atom or group that differs from the atom or group found in a naturally occurring nucleoside (e.g., a modified 2′-substuent is any atom or group at the 2′-position of a nucleoside other than H or OH). Substituent groups can be protected or unprotected. In certain embodiments, compounds of the present invention have substituents at one or at more than one position of the parent compound. Substituents may also be further substituted with other substituent groups and may be attached directly or via a linking group such as an alkyl or hydrocarbyl group to a parent compound.

Likewise, as used herein, “substituent” in reference to a chemical functional group means an atom or group of atoms differs from the atom or a group of atoms normally present in the named functional group. In certain embodiments, a substituent replaces a hydrogen atom of the functional group (e.g., in certain embodiments, the substituent of a substituted methyl group is an atom or group other than hydrogen which replaces one of the hydrogen atoms of an unsubstituted methyl group). Unless otherwise indicated, groups amenable for use as substituents include without limitation, halogen, hydroxyl, alkyl, alkenyl, alkynyl, acyl (—C(O)R_(aa)), carboxyl (—C(O)O—R_(aa)), aliphatic groups, alicyclic groups, alkoxy, substituted oxy (—O—R_(aa)), aryl, aralkyl, heterocyclic radical, heteroaryl, heteroarylalkyl, amino (—N(R_(bb))(R_(cc))), imino(═NR_(bb)), amido (—C(O)N(R_(bb))(R_(cc)) or —N(R_(bb))C(O)R_(aa)), azido (—N₃), nitro (—NO₂), cyano (—CN), carbamido (—OC(O)N(R_(bb))(R_(cc)) or —N(R_(bb))C(O)OR_(aa)), ureido (—N(R_(bb))C(O)N(R_(bb))(R_(cc))), thioureido (—N(R_(bb))C(S)N(R_(bb))—(R_(cc))), guanidinyl (—N(R_(bb))C(═NR_(bb))N(R_(bb))(R_(cc))), amidinyl (—C(═NR_(bb))N(R_(bb))(R_(cc)) or —N(R_(bb))C(═NR_(bb))(R_(aa))), thiol (—SR_(bb)), sulfinyl (—S(O)R_(bb)), sulfonyl (—S(O)₂R_(bb)) and sulfonamidyl (—S(O)₂N(R_(bb))(R_(cc)) or —N(R_(bb))S—(O)₂R_(bb)). Wherein each R_(aa), R_(bb) and R_(cc) is, independently, H, an optionally linked chemical functional group or a further substituent group with a preferred list including without limitation, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl. Selected substituents within the compounds described herein are present to a recursive degree.

As used herein, “alkyl,” as used herein, means a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms. Examples of alkyl groups include without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl, dodecyl and the like. Alkyl groups typically include from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms (C₁-C₁₂ alkyl) with from 1 to about 6 carbon atoms being more preferred.

As used herein, “alkenyl,” means a straight or branched hydrocarbon chain radical containing up to twenty four carbon atoms and having at least one carbon-carbon double bond. Examples of alkenyl groups include without limitation, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, dienes such as 1,3-butadiene and the like. Alkenyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkenyl groups as used herein may optionally include one or more further substituent groups.

As used herein, “alkynyl,” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms and having at least one carbon-carbon triple bond. Examples of alkynyl groups include, without limitation, ethynyl, 1-propynyl, 1-butynyl, and the like. Alkynyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkynyl groups as used herein may optionally include one or more further substituent groups.

As used herein, “acyl,” means a radical formed by removal of a hydroxyl group from an organic acid and has the general Formula —C(O)—X where X is typically aliphatic, alicyclic or aromatic. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates, aliphatic phosphates and the like. Acyl groups as used herein may optionally include further substituent groups.

As used herein, “alicyclic” means a cyclic ring system wherein the ring is aliphatic. The ring system can comprise one or more rings wherein at least one ring is aliphatic. Preferred alicyclics include rings having from about 5 to about 9 carbon atoms in the ring. Alicyclic as used herein may optionally include further substituent groups.

As used herein, “aliphatic” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms wherein the saturation between any two carbon atoms is a single, double or triple bond. An aliphatic group preferably contains from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms with from 1 to about 6 carbon atoms being more preferred. The straight or branched chain of an aliphatic group may be interrupted with one or more heteroatoms that include nitrogen, oxygen, sulfur and phosphorus. Such aliphatic groups interrupted by heteroatoms include without limitation, polyalkoxys, such as polyalkylene glycols, polyamines, and polyimines. Aliphatic groups as used herein may optionally include further substituent groups.

As used herein, “alkoxy” means a radical formed between an alkyl group and an oxygen atom wherein the oxygen atom is used to attach the alkoxy group to a parent molecule. Examples of alkoxy groups include without limitation, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy, tert-butoxy, n-pentoxy, neopentoxy, n-hexoxy and the like. Alkoxy groups as used herein may optionally include further substituent groups.

As used herein, “aminoalkyl” means an amino substituted C₁-C₁₂ alkyl radical. The alkyl portion of the radical forms a covalent bond with a parent molecule. The amino group can be located at any position and the aminoalkyl group can be substituted with a further substituent group at the alkyl and/or amino portions.

As used herein, “aralkyl” and “arylalkyl” mean an aromatic group that is covalently linked to a C₁-C₁₂ alkyl radical. The alkyl radical portion of the resulting aralkyl (or arylalkyl) group forms a covalent bond with a parent molecule. Examples include without limitation, benzyl, phenethyl and the like. Aralkyl groups as used herein may optionally include further substituent groups attached to the alkyl, the aryl or both groups that form the radical group.

As used herein, “aryl” and “aromatic” mean a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings. Examples of aryl groups include without limitation, phenyl, naphthyl, tetrahydronaphthyl, indanyl, idenyl and the like. Preferred aryl ring systems have from about 5 to about 20 carbon atoms in one or more rings. Aryl groups as used herein may optionally include further substituent groups.

As used herein, “halo” and “halogen,” mean an atom selected from fluorine, chlorine, bromine and iodine.

As used herein, “heteroaryl,” and “heteroaromatic,” mean a radical comprising a mono- or polycyclic aromatic ring, ring system or fused ring system wherein at least one of the rings is aromatic and includes one or more heteroatoms. Heteroaryl is also meant to include fused ring systems including systems where one or more of the fused rings contain no heteroatoms. Heteroaryl groups typically include one ring atom selected from sulfur, nitrogen or oxygen. Examples of heteroaryl groups include without limitation, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl and the like. Heteroaryl radicals can be attached to a parent molecule directly or through a linking moiety such as an aliphatic group or hetero atom. Heteroaryl groups as used herein may optionally include further substituent groups.

As used herein, “huntingtin transcript” means a transcript transcribed from a huntingtin gene.

B. Oligomeric Compounds

In certain embodiments, the present invention provides oligomeric compounds. In certain embodiments, such oligomeric compounds comprise oligonucleotides optionally comprising one or more conjugate and/or terminal groups. In certain embodiments, an oligomeric compound consists of an oligonucleotide. In certain embodiments, oligonucleotides comprise one or more chemical modifications. Such chemical modifications include modifications of one or more nucleoside (including modifications to the sugar moiety and/or the nucleobase) and/or modifications to one or more internucleoside linkage.

a. Certain Modified Nucleosides

In certain embodiments, provided herein are oligomeric compounds comprising or consisting of oligonucleotides comprising at least one modified nucleoside. Such modified nucleosides comprise a modified sugar moeity, a modified nucleobase, or both a modified sugar moiety and a modified nucleobase.

i. Certain Modified Sugar Moieties

In certain embodiments, compounds of the invention comprise one or more modified nucleosides comprising a modified sugar moiety. Such compounds comprising one or more sugar-modified nucleosides may have desirable properties, such as enhanced nuclease stability or increased binding affinity with a target nucleic acid relative to an oligonucleotide comprising only nucleosides comprising naturally occurring sugar moieties. In certain embodiments, modified sugar moieties are substituted sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of substituted sugar moieties.

In certain embodiments, modified sugar moieties are substituted sugar moieties comprising one or more non-bridging sugar substituent, including but not limited to substituents at the 2′ and/or 5′ positions. Examples of sugar substituents suitable for the 2′-position, include, but are not limited to: 2′-F, 2′-OCH₃ (“OMe” or “O-methyl”), and 2′-O(CH₂)₂OCH₃ (“MOE”). In certain embodiments, sugar substituents at the 2′ position is selected from allyl, amino, azido, thio, O-allyl, O—C₁-C₁₀ alkyl, O—C₁-C₁₀ substituted alkyl; OCF₃, O(CH₂)₂SCH₃, O(CH₂)₂—O—N(R_(m))(R_(n)), and O—CH₂—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C₁-C₁₀ alkyl. Examples of sugar substituents at the 5′-position, include, but are not limited to: 5′-methyl (R or S); 5′-vinyl, and 5′-methoxy. In certain embodiments, substituted sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties (see, e.g., PCT International Application WO 2008/101157, for additional 5′, 2′-bis substituted sugar moieties and nucleosides).

Nucleosides comprising 2′-substituted sugar moieties are referred to as 2′-substituted nucleosides. In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from halo, allyl, amino, azido, SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl. These 2′-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from F, NH₂, N₃, OCF₃, O—CH₃, O(CH₂)₃NH₂, CH₂—CH═CH₂, O—CH₂—CH═CH₂, OCH₂CH₂OCH₃, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)), O(CH₂)₂O(CH₂)₂N(CH₃)₂, and N-substituted acetamide (O—CH₂—C(═O)—N(R_(m))(R_(n)) where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl.

In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF₃, O—CH₃, OCH₂CH₂OCH₃, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(CH₃)₂, —O(CH₂)₂O(CH₂)₂N(CH₃)₂, and O—CH₂—C(═O)—N(H)CH₃.

In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, O—CH₃, and OCH₂CH₂OCH₃.

Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ sugar substituents, include, but are not limited to: —[C(R_(a))(R_(b))]_(n)—, —[C(R_(a))(R_(b))]_(n)—O—, —C(R_(a)R_(b))—N(R)—O— or, —C(R_(a)R_(b))—O—N(R)—; 4′- CH₂-2′, 4′-(CH₂)₂-2′, 4′-(CH₂)₃-2′, 4′-(CH₂)—O-2′ (LNA); 4′-(CH₂)—S-2′; 4′-(CH₂)₂—O-2′ (ENA); 4′-CH(CH₃)—O-2′ (cEt) and 4′-CH(CH₂OCH₃)—O-2′,and analogs thereof (see, e.g., U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-C(CH₃)(CH₃)—O-2′ and analogs thereof, (see, e.g., WO2009/006478, published Jan. 8, 2009); 4′-CH₂—N(OCH₃)-2′ and analogs thereof (see, e.g., WO2008/150729, published Dec. 11, 2008); 4′-CH₂—O—N(CH₃)-2′ (see, e.g., US2004/0171570, published Sep. 2, 2004); 4′-CH₂—O—N(R)-2′, and 4′-CH₂—N(R)-0-2′-, wherein each R is, independently, H, a protecting group, or C₁-C₁₂ alkyl; 4′-CH₂—N(R)—O-2′, wherein R is H, C₁-C₁₂ alkyl, or a protecting group (see, U.S. Pat. No. 7,427,672, issued on Sep. 23, 2008); 4′-CH₂—C(H)(CH₃)-2′ (see, e.g., Chattopadhyaya, et al., J. Org. Chem., 2009, 74, 118-134); and 4′-CH₂—C(═CH₂)-2′ and analogs thereof (see, published PCT International Application WO 2008/154401, published on Dec. 8, 2008).

In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(R_(a))(R_(b))]_(n)—, —C(R_(a))═C(R_(b))—, —C(R_(a))═N—, —C(═NR_(a))—, —C(═O)—, —C(═S)—, —O—, —Si(R_(a))₂—, —S(═O)_(x)—, and —N(R_(a))—;

wherein:

x is 0, 1, or 2;

n is 1, 2, 3, or 4;

each R_(a) and R_(b) is, independently, H, a protecting group, hydroxyl, C₁-C₁₂ alkyl, substituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, substituted C₂-C₁₂ alkenyl, C₂-C₁₂ alkynyl, substituted C₂-C₁₂ alkynyl, C₅-C₂₀ aryl, substituted C₅-C₂₀ aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C₅-C₇ alicyclic radical, substituted C₅-C₇ alicyclic radical, halogen, OJ₁, NJ₁J₂, SJ₁, N₃, COOJ₁, acyl (C(═O)—H), substituted acyl, CN, sulfonyl (S(═O)₂-J₁), or sulfoxyl (S(═O)-J₁); and

each J₁ and J₂ is, independently, H, C₁-C₁₂ alkyl, substituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, substituted C₂-C₁₂ alkenyl, C₂-C₁₂ alkynyl, substituted C₂-C₁₂ alkynyl, C₅-C₂₀ aryl, substituted C₅-C₂₀ aryl, acyl (C(═O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C₁-C₁₂ aminoalkyl, substituted C₁-C₁₂ aminoalkyl, or a protecting group.

Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) α-L-Methyleneoxy (4′-CH₂—O-2′) BNA, (B) β-D-Methyleneoxy (4′-CH₂—O-2′) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4′-(CH₂)₂—O-2′) BNA, (D) Aminooxy (4′-CH₂—O—N(R)-2′) BNA, (E) Oxyamino (4′-CH₂—N(R)—O-2′) BNA, (F) Methyl(methyleneoxy) (4′-CH(CH₃)—O-2′) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4′-CH₂—S-2′) BNA, (H) methylene-amino (4′-CH₂—N(R)-2′) BNA, (I) methyl carbocyclic (4′-CH₂—CH(CH₃)-2′) BNA, (J) propylene carbocyclic (4′-(CH₂)₃-2′) BNA, and (K) Ethylene(methoxy) (4′-(CH(CH₂OMe)-O-2′) BNA (also referred to as constrained MOE or cMOE) as depicted below.

wherein Bx is a nucleobase moiety and R is, independently, H, a protecting group, or C₁-C₁₂ alkyl.

Additional bicyclic sugar moieties are known in the art, for example: Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A, 2000, 97, 5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J Am. Chem. Soc., 129(26) 8362-8379 (Jul. 4, 2007); Elayadi et al., Curr. Opinion Invens. Drugs, 2001, 2, 558-561; Braasch et al., Chem. Biol., 2001, 8, 1-7; Orum et al., Curr. Opinion Mol. Ther., 2001, 3, 239-243; U.S. Pat. Nos. 7,053,207, 6,268,490, 6,770,748, 6,794,499, 7,034,133, 6,525,191, 6,670,461, and 7,399,845; WO 2004/106356, WO 1994/14226, WO 2005/021570, and WO 2007/134181; U.S. Patent Publication Nos. US2004/0171570, US2007/0287831, and US2008/0039618; U.S. patent Ser. Nos. 12/129,154, 60/989,574, 61/026,995, 61/026,998, 61/056,564, 61/086,231, 61/097,787, and 61/099,844; and PCT International Applications Nos. PCT/US2008/064591, PCT/US2008/066154, and PCT/US2008/068922.

In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, a nucleoside comprising a 4′-2′ methylene-oxy bridge, may be in the α-L configuration or in the β-D configuration. Previously, α-L-methyleneoxy (4′-CH₂—O-2′) bicyclic nucleosides have been incorporated into antisense oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).

In certain embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars). (see, PCT International Application WO 2007/134181, published on Nov. 22, 2007, wherein LNA is substituted with, for example, a 5′-methyl or a 5′-vinyl group).

In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the naturally occuring sugar is substituted, e.g., with a sulfer, carbon or nitrogen atom. In certain such embodiments, such modified sugar moiety also comprises bridging and/or non-bridging substituents as described above. For example, certain sugar surogates comprise a 4′-sulfer atom and a substitution at the 2′-position (see, e.g., published U.S. Patent Application US2005/0130923, published on Jun. 16, 2005) and/or the 5′ position. By way of additional example, carbocyclic bicyclic nucleosides having a 4′-2′ bridge have been described (see, e.g., Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al., J Org. Chem., 2006, 71, 7731-7740).

In certain embodiments, sugar surrogates comprise rings having other than 5-atoms. For example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran. Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), manitol nucleic acid (MNA) (see Leumann, C J. Bioorg. &Med. Chem. (2002) 10:841-854), fluoro HNA (F-HNA), and those compounds having Formula VII:

wherein independently for each of said at least one tetrahydropyran nucleoside analog of Formula VII:

Bx is a nucleobase moiety;

T₃ and T₄ are each, independently, an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound or one of T₃ and T₄ is an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound and the other of T₃ and T₄ is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group;

q₁, q₂, q₃, q₄, q₅, q₆ and q₇ are each, independently, H, C₁-C₆ alkyl, substituted C₁-C₆ alkyl, C₂-C₆ alkenyl, substituted C₂-C₆ alkenyl, C₂-C₆ alkynyl, or substituted C₂-C₆ alkynyl; and

each of R₁ and R₂ is independently selected from among: hydrogen, halogen, substituted or unsubstituted alkoxy, NJ₁J₂, SJ₁, N₃, OC(═X)J₁, OC(═X)NJ₁J₂, NJ₃C(═X)NJ₁J₂, and CN, wherein X is O, S or NJ₁, and each J₁, J₂, and J₃ is, independently, H or C₁-C₆ alkyl.

In certain embodiments, the modified THP nucleosides of Formula VII are provided wherein q₁, q₂, q₃, q₄, q₅, q₆ and q₇ are each H. In certain embodiments, at least one of q₁, q₂, q₃, q₄, q₅, q₆ and q₇ is other than H. In certain embodiments, at least one of q₁, q₂, q₃, q₄, q₅, q₆ and q₇ is methyl. In certain embodiments, THP nucleosides of Formula VII are provided wherein one of R₁ and R₂ is F. In certain embodiments, R₁ is fluoro and R₂ is H, R₁ is methoxy and R₂ is H, and R₁ is methoxyethoxy and R₂ is H.

Many other bicyclo and tricyclo sugar surrogate ring systems are also known in the art that can be used to modify nucleosides for incorporation into antisense compounds (see, e.g., review article: Leumann, J. C, Bioorganic & Medicinal Chemistry, 2002, 10, 841-854).

Combinations of modifications are also provided without limitation, such as 2′-F-5′-methyl substituted nucleosides (see PCT International Application WO 2008/101157 Published on Aug. 21, 2008 for other disclosed 5′, 2′-bis substituted nucleosides) and replacement of the ribosyl ring oxygen atom with S and further substitution at the 2′-position (see published U.S. Patent Application US2005-0130923, published on Jun. 16, 2005) or alternatively 5′-substitution of a bicyclic nucleic acid (see PCT International Application WO 2007/134181, published on Nov. 22, 2007 wherein a 4′-CH₂—O-2′ bicyclic nucleoside is further substituted at the 5′ position with a 5′-methyl or a 5′-vinyl group). The synthesis and preparation of carbocyclic bicyclic nucleosides along with their oligomerization and biochemical studies have also been described (see, e.g., Srivastava et al., J. Am. Chem. Soc. 2007, 129(26), 8362-8379).

In certain embodiments, the present invention provides oligonucleotides comprising modified nucleosides. Those modified nucleotides may include modified sugars, modified nucleobases, and/or modified linkages. The specific modifications are selected such that the resulting oligonucleotides possess desireable characteristics. In certain embodmiments, oligonucleotides comprise one or more RNA-like nucleosides. In certain embodiments, oligonucleotides comprise one or more DNA-like nucleotides.

ii. Certain Modified Nucleobases

In certain embodiments, nucleosides of the present invention comprise one or more unmodified nucleobases. In certain embodiments, nucleosides of the present invention comprise one or more modified nucleobases.

In certain embodiments, modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil; 5-propynylcytosine; 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl (—C≡C—CH₃) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine, 3-deazaguanine and 3-deazaadenine, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288.

Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121; 5,596,091; 5,614,617; 5,645,985; 5,681,941; 5,750,692; 5,763,588; 5,830,653 and 6,005,096, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

b. Certain Internucleoside Linkages

In certain embodiments, nucleosides may be linked together using any internucleoside linkage to form oligonucleotides. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (P═O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P═S). Representative non-phosphorus containing internucleoside linking groups include, but are not limited to, methylenemethylimino (—CH₂—N(CH₃)—O—CH₂—), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)₂—O—); and N,N′-dimethylhydrazine (—CH₂—N(CH₃)—N(CH₃)—). Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.

The oligonucleotides described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), α or β such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.

Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH₂—N(CH₃)—O-5′), amide-3 (3′-CH₂—C(═O)—N(H)-5′), amide-4 (3′-CH₂—N(H)—C(═O)-5′), formacetal (3′-O—CH₂—O-5′), and thioformacetal (3′-S—CH₂—O-5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH₂ component parts.

i. 3′-Endo Modifications

In one aspect of the present disclosure, oligomeric compounds include nucleosides synthetically modified to induce a 3′-endo sugar conformation. A nucleoside can incorporate synthetic modifications of the heterocyclic base moiety, the sugar moiety or both to induce a desired 3′-endo sugar conformation. These modified nucleosides are used to mimic RNA like nucleosides so that particular properties of an oligomeric compound can be enhanced while maintaining the desirable 3′-endo conformational geometry. There is an apparent preference for an RNA type duplex (A form helix, predominantly 3′-endo) as a requirement of RNA interference which is supported in part by the fact that duplexes composed of 2′-deoxy-2′-F-nucleosides appear efficient in triggering RNAi response in the C. elegans system. Properties that are enhanced by using more stable 3′-endo nucleosides include but aren't limited to modulation of pharmacokinetic properties through modification of protein binding, protein off-rate, absorption and clearance; modulation of nuclease stability as well as chemical stability; modulation of the binding affinity and specificity of the oligomer (affinity and specificity for enzymes as well as for complementary sequences); and increasing efficacy of RNA cleavage. The present invention provides oligomeric compounds having one or more nucleosides modified in such a way as to favor a C3′-endo type conformation.

Nucleoside conformation is influenced by various factors including substitution at the 2′, 3′ or 4′-positions of the pentofuranosyl sugar. Electronegative substituents generally prefer the axial positions, while sterically demanding substituents generally prefer the equatorial positions (Principles of Nucleic Acid Structure, Wolfgang Sanger, 1984, Springer-Verlag.) Modification of the 2′ position to favor the 3′-endo conformation can be achieved while maintaining the 2′-OH as a recognition element, as exemplified in Example 35, below (Gallo et al., Tetrahedron (2001), 57, 5707-5713. Harry-O'kuru et al., J. Org. Chem., (1997), 62(6), 1754-1759 and Tang et al., J. Org. Chem. (1999), 64, 747-754.) Alternatively, preference for the 3′-endo conformation can be achieved by deletion of the 2′-OH as exemplified by 2′deoxy-2′F-nucleosides (Kawasaki et al., J. Med. Chem. (1993), 36, 831-841), which adopts the 3′-endo conformation positioning the electronegative fluorine atom in the axial position. Other modifications of the ribose ring, for example substitution at the 4′-position to give 4′-F modified nucleosides (Guillerm et al., Bioorganic and Medicinal Chemistry Letters (1995), 5, 1455-1460 and Owen et al., J. Org. Chem. (1976), 41, 3010-3017), or for example modification to yield methanocarba nucleoside analogs (Jacobson et al., J. Med. Chem. Lett. (2000), 43, 2196-2203 and Lee et al., Bioorganic and Medicinal Chemistry Letters (2001), 11, 1333-1337) also induce preference for the 3′-endo conformation. Some modifications actually lock the conformational geometry by formation of a bicyclic sugar moiety e.g. locked nucleic acid (LNA, Singh et al, Chem. Commun. (1998), 4, 455-456), and ethylene bridged nucleic acids (ENA, Morita et al, Bioorganic & Medicinal Chemistry Letters (2002), 12, 73-76.)

c. Certain Motifs

In certain embodiments, oligomeric compounds comprise or consist of oligonucleotides. In certain embodiments, such oligonucleotides comprise one or more chemical modification. In certain embodiments, chemically modified oligonucleotides comprise one or more modified sugars. In certain embodiments, chemically modified oligonucleotides comprise one or more modified nucleobases. In certain embodiments, chemically modified oligonucleotides comprise one or more modified internucleoside linkages. In certain embodiments, the chemical modifications (sugar modifications, nucleobase modifications, and/or linkage modifications) define a pattern or motif. In certain embodiments, the patterns of chemical modifications of sugar moieties, internucleoside linkages, and nucleobases are each independent of one another. Thus, an oligonucleotide may be described by its sugar modification motif, internucleoside linkage motif and/or nucleobase modification motif (as used herein, nucleobase modification motif describes the chemical modifications to the nucleobases independent of the sequence of nucleobases).

i. Certain Sugar Motifs

In certain embodiments, oligonucleotides comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar motif. Such sugar motifs include but are not limited to any of the sugar modifications discussed herein.

In certain embodiments, the oligonucleotides comprise or consist of a region having a gapmer sugar motif, which comprises two external regions or “wings” and a central or internal region or “gap.” The three regions of a gapmer sugar motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap. Specifically, at least the sugar moieties of the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap. In certain embodiments, the sugar moieties within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap. In certain embodiments, the sugar motifs of the two wings are the same as one another (symmetric sugar gapmer). In certain embodiments, the sugar motifs of the 5′-wing differs from the sugar motif of the 3′-wing (asymmetric sugar gapmer).

ii. Certain Nucleobase Modification Motifs

In certain embodiments, oligonucleotides comprise chemical modifications to nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or nucleobases modification motif. In certain embodiments, each nucleobase is modified. In certain embodiments, none of the nucleobases is chemically modified.

In certain embodiments, oligonucleotides comprise a block of modified nucleobases. In certain such embodiments, the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 3′-end of the oligonucleotide. In certain such embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 5′-end of the oligonucleotide.

In certain embodiments, nucleobase modifications are a function of the natural base at a particular position of an oligonucleotide. For example, in certain embodiments each purine or each pyrimidine in an oligonucleotide is modified. In certain embodiments, each adenine is modified. In certain embodiments, each guanine is modified. In certain embodiments, each thymine is modified. In certain embodiments, each cytosine is modified. In certain embodiments, each uracil is modified.

In certain embodiments, oligonucleotides comprise one or more nucleosides comprising a modified nucleobase. In certain embodiments, oligonucleotides having a gapmer sugar motif comprise a nucleoside comprising a modified nucleobase. In certain such embodiments, one nucleoside comprising a modified nucleobases is in the central gap of an oligonucleotide having a gapmer sugar motif. In certain embodiments, the sugar is an unmodified 2′deoxynucleoside. In certain embodiments, the modified nucleobase is selected from: a 2-thio pyrimidine and a 5-propyne pyrimidine

In certain embodiments, some, all, or none of the cytosine moieties in an oligonucleotide are 5-methyl cytosine moieties. Herein, 5-methyl cytosine is not a “modified nucleobase.” Accordingly, unless otherwise indicated, unmodified nucleobases include both cytosine residues having a 5-methyl and those lacking a 5 methyl. In certain embodiments, the methylation state of all or some cytosine nucleobases is specified.

iii. Certain Nucleoside Motifs

In certain embodiments, oligonucleotides comprise nucleosides comprising modified sugar moieties and/or nucleosides comprising modified nucleobases. Such motifs can be described by their sugar motif and their nucleobase motif separately or by their nucleoside motif, which provides positions or patterns of modified nucleosides (whether modified sugar, nucleobase, or both sugar and nucleobase) in an oligonucleotide.

In certain embodiments, the oligonucleotides comprise or consist of a region having a gapmer nucleoside motif, which comprises two external regions or “wings” and a central or internal region or “gap.” The three regions of a gapmer nucleoside motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties and/or nucleobases of the nucleosides of each of the wings differ from at least some of the sugar moieties and/or nucleobase of the nucleosides of the gap. Specifically, at least the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the neighboring gap nucleosides, thus defining the boundary between the wings and the gap. In certain embodiments, the nucleosides within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside that differs from one or more other nucleosides of the gap. In certain embodiments, the nucleoside motifs of the two wings are the same as one another (symmetric gapmer). In certain embodiments, the nucleoside motifs of the 5′-wing differs from the nucleoside motif of the 3′-wing (asymmetric gapmer).

iv. Certain 5′-Wings

In certain embodiments, the 5′-wing of a gapmer consists of 1 to 6 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 5′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 6 linked nucleosides.

In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least two bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least three bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least four bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one LNA nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a bicyclic nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a constrained ethyl nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a LNA nucleoside.

In certain embodiments, the 5′-wing of a gapmer comprises at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-OMe nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a non-bicyclic modified nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-substituted nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-MOE nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-OMe nucleoside.

In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-deoxynucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-deoxynucleoside. In a certain embodiments, the 5′-wing of a gapmer comprises at least one ribonucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a ribonucleoside. In certain embodiments, one, more than one, or each of the nucleosides of the 5′-wing is an RNA-like nucleoside.

In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing ofa gapmer comprises at least one bicyclic nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-deoxynucleoside.

In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-deoxynucleoside.

In certain embodiments, the 5′-wing of a gapmer has a nucleoside motif selected from among the following: ADDA; ABDAA; ABBA; ABB; ABAA; AABAA; AAABAA; AAAABAA; AAAAABAA; AAABAA; AABAA; ABAB; ABADB; ABADDB; AAABB; AAAAA; ABBDC; ABDDC; ABBDCC; ABBDDC; ABBDCC; ABBC; AA; AAA; AAAA; AAAAB; AAAAAAA; AAAAAAAA; ABBB; AB; ABAB; AAAAB; AABBB; AAAAB; and AABBB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, each C is a modified nucleoside of a third type, and each D is an unmodified deoxynucleoside.

In certain embodiments, the 5′-wing of a gapmer has a nucleoside motif selected from among the following: AB, ABB, AAA, BBB, BBBAA, AAB, BAA, BBAA, AABB, AAAB, ABBW, ABBWW, ABBB, ABBBB, ABAB, ABABAB, ABABBB, ABABAA, AAABB, AAAABB, AABB, AAAAB, AABBB, ABBBB, BBBBB, AAABW, AAAAA, BBBBAA, and AAABW; wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of either the first type, the second type or a third type.

In certain embodiments, the 5′-wing of a gapmer has a nucleoside motif selected from among the following: ABB; ABAA; AABAA; AAABAA; ABAB; ABADB; AAABB; AAAAA; AA; AAA; AAAA; AAAAB; ABBB; AB; and ABAB; wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of either the first type, the second type or a third type.

In certain embodiments, an oligonucleotide comprises any 5′-wing motif provided herein. In certain such embodiments, the oligonucleotide is a 5′-hemimer (does not comprise a 3′-wing). In certain embodiments, such an oligonucleotide is a gapmer. In certain such embodiments, the 3′-wing of the gapmer may comprise any nucleoside motif.

In certain embodiments, the 5′-wing of a gapmer has a sugar motif selected from among those listed in the following non-limiting tables:

TABLE 1 Certain 5′-Wing Sugar Motifs Certain 5′-Wing Sugar Motifs AAAAA ABCBB BABCC BCBBA CBACC AAAAB ABCBC BACAA BCBBB CBBAA AAAAC ABCCA BACAB BCBBC CBBAB AAABA ABCCB BACAC BCBCA CBBAC AAABB ABCCC BACBA BCBCB CBBBA AAABC ACAAA BACBB BCBCC CBBBB AAACA ACAAB BACBC BCCAA CBBBC AAACB ACAAC BACCA BCCAB CBBCA AAACC ACABA BACCB BCCAC CBBCB AABAA ACABB BACCC BCCBA CBBCC AABAB ACABC BBAAA BCCBB CBCAA AABAC ACACA BBAAB BCCBC CBCAB AABBA ACACB BBAAC BCCCA CBCAC AABBB ACACC BBABA BCCCB CBCBA AABBC ACBAA BBABB BCCCC CBCBB AABCA ACBAB BBABC CAAAA CBCBC AABCB ACBAC BBACA CAAAB CBCCA AABCC ACBBA BBACB CAAAC CBCCB AACAA ACBBB BBACC CAABA CBCCC AACAB ACBBC BBBAA CAABB CCAAA AACAC ACBCA BBBAB CAABC CCAAB AACBA ACBCB BBBAC CAACA CCAAC AACBB ACBCC BBBBA CAACB CCABA AACBC ACCAA BBBBB CAACC CCABB AACCA ACCAB BBBBC CABAA CCABC AACCB ACCAC BBBCA CABAB CCACA AACCC ACCBA BBBCB CABAC CCACB ABAAA ACCBB BBBCC CABBA CCACC ABAAB ACCBC BBCAA CABBB CCBAA ABAAC ACCCA BBCAB CABBC CCBAB ABABA ACCCB BBCAC CABCA CCBAC ABABB ACCCC BBCBA CABCB CCBBA ABABC BAAAA BBCBB CABCC CCBBB ABACA BAAAB BBCBC CACAA CCBBC ABACB BAAAC BBCCA CACAB CCBCA ABACC BAABA BBCCB CACAC CCBCB ABBAA BAABB BBCCC CACBA CCBCC ABBAB BAABC BCAAA CACBB CCCAA ABBAC BAACA BCAAB CACBC CCCAB ABBBA BAACB BCAAC CACCA CCCAC ABBBB BAACC BCABA CACCB CCCBA ABBBC BABAA BCABB CACCC CCCBB ABBCA BABAB BCABC CBAAA CCCBC ABBCB BABAC BCACA CBAAB CCCCA ABBCC BABBA BCACB CBAAC CCCCB ABCAA BABBB BCACC CBABA CCCCC ABCAB BABBC BCBAA CBABB ABCAC BABCA BCBAB CBABC ABCBA BABCB BCBAC CBACA

TABLE 2 Certain 5′-Wing Sugar Motifs Certain 5′-Wing Sugar Motifs AAAAA BABC CBAB ABBB BAA AAAAB BACA CBAC BAAA BAB AAABA BACB CBBA BAAB BBA AAABB BACC CBBB BABA BBB AABAA BBAA CBBC BABB AA AABAB BBAB CBCA BBAA AB AABBA BBAC CBCB BBAB AC AABBB BBBA CBCC BBBA BA ABAAA BBBB CCAA BBBB BB ABAAB BBBC CCAB AAA BC ABABA BBCA CCAC AAB CA ABABB BBCB CCBA AAC CB ABBAA BBCC CCBB ABA CC ABBAB BCAA CCBC ABB AA ABBBA BCAB CCCA ABC AB ABBBB BCAC CCCB ACA BA BAAAA ABCB BCBA ACB BAAAB ABCC BCBB ACC BAABA ACAA BCBC BAA BAABB ACAB BCCA BAB BABAA ACAC BCCB BAC BABAB ACBA BCCC BBA BABBA ACBB CAAA BBB BABBB ACBC CAAB BBC BBAAA ACCA CAAC BCA BBAAB ACCB CABA BCB BBABA ACCC CABB BCC BBABB BAAA CABC CAA BBBAA BAAB CACA CAB BBBAB BAAC CACB CAC BBBBA BABA CACC CBA BBBBB BABB CBAA CBB AAAA AACC CCCC CBC AAAB ABAA AAAA CCA AAAC ABAB AAAB CCB AABA ABAC AABA CCC AABB ABBA AABB AAA AABC ABBB ABAA AAB AACA ABBC ABAB ABA AACB ABCA ABBA ABB

In certain embodiments, each A, each B, and each C located at the 3′-most 5′-wing nucleoside is a modified nucleoside. For example, in certain embodiments the 5′-wing motif is selected from among ABB, BBB, and CBB, wherein the underlined nucleoside represents the 3′-most 5′-wing nucleoside and wherein the underlined nucleoside is a modified nucleoside. In certain embodiments, the the 3′-most 5′-wing nucleoside comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, the the 3′-most 5′-wing nucleoside comprises a bicyclic sugar moiety selected from among cEt and LNA. In certain embodiments, the the 3′-most 5′-wing nucleoside comprises cEt. In certain embodiments, the the 3′-most 5′-wing nucleoside comprises LNA.

In certain embodiments, each A comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each A comprises a modified sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, ara-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each A comprises a bicyclic sugar moiety. In certain embodiments, each A comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises a modified nucleobase. In certain embodiments, each A comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne uridine nucleoside. In certain embodiments, each A comprises an HNA. In certain embodiments, each A comprises a F-HNA. In certain embodiments, each A comprises a 5′-substituted sugar moiety selected from among 5′-Me DNA, and 5′-(R)-Me DNA.

In certain embodiments, each B comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each B comprises a modified sugar moiety. In certain embodiments, each B comprises a 2′-substituted sugar moiety. In certain embodiments, each B comprises a 2′-subsituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each B comprises a bicyclic sugar moiety. In certain embodiments, each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each B comprises a modified nucleobase. In certain embodiments, each B comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne urindine nucleoside. In certain embodiments, each B comprises an HNA. In certain embodiments, each B comprises a F-HNA. In certain embodiments, each B comprises a 5′-substituted sugar moiety selected from among 5′-Me DNA, and 5′-(R)-Me DNA.

In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, ara-F, OCH₃ and O(CH₂)₂—OCH₃ and each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises O(CH₂)₂—OCH₃ and each B comprises cEt.

In certain embodiments, each C comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each C comprises a modified sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each C comprises a 5′-substituted sugar moiety. In certain embodiments, each C comprises a 5′-substituted sugar moiety selected from among 5′-Me DNA, and 5′-(R)-Me DNA. In certain embodiments, each C comprises a bicyclic sugar moiety. In certain embodiments, each C comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each C comprises a modified nucleobase.

In certain embodiments, each C comprises a modified nucleobase selected from among 2-thio-thymidine and 5-propyne uridine. In certain embodiments, each C comprises a 2-thio-thymidine nucleoside. In certain embodiments, each C comprises an HNA. In certain embodiments, each C comprises an F-HNA.

v. Certain 3′-Wings

In certain embodiments, the 3′-wing of a gapmer consists of 1 to 6 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 3′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 6 linked nucleosides.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a bicyclic nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a constrained ethyl nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a LNA nucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least two non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least three non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least four non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-OMe nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a non-bicyclic modified nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-substituted nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-MOE nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-OMe nucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-deoxynucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-deoxynucleoside. In a certain embodiments, the 3′-wing of a gapmer comprises at least one ribonucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a ribonucleoside. In certain embodiments, one, more than one, or each of the nucleosides of the 5′-wing is an RNA-like nucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing ofa gapmer comprises at least one bicyclic nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside.

In certain embodiments, the 3′-wing of a gapmer has a nucleoside motif selected from among the following: ABB, ABAA, AAABAA, AAAAABAA, AABAA, AAAABAA, AAABAA, ABAB, AAAAA, AAABB, AAAAAAAA, AAAAAAA, AAAAAA, AAAAB, AAAA, AAA, AA, AB, ABBB, ABAB, AABBB; wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type. In certain embodiments, an oligonucleotide comprises any 3′-wing motif provided herein. In certain such embodiments, the oligonucleotide is a 3′-hemimer (does not comprise a 5′-wing). In certain embodiments, such an oligonucleotide is a gapmer. In certain such embodiments, the 5′-wing of the gapmer may comprise any nucleoside motif.

In certain embodiments, the 3′-wing of a gapmer has a nucleoside motif selected from among the following: BBA, AAB, AAA, BBB, BBAA, AABB, WBBA, WAAB, BBBA, BBBBA, BBBB, BBBBBA, ABBBBB, BBAAA, AABBB, BBBAA, BBBBA, BBBBB, BABA, AAAAA, BBAAAA, AABBBB, BAAAA, and ABBBB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of either the first type, the second type or a third type.

In certain embodiments, the 3′-wing of a gapmer has a nucleoside motif selected from among the following: ABB; AAABAA; AABAA; AAAABAA; AAAAA; AAABB; AAAAAAAA; AAAAAAA; AAAAAA; AAAAB; AB; ABBB; and ABAB, wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type, and each W is a modified nucleoside of either the first type, the second type or a third type.

In certain embodiments, the 3′-wing of a gapmer has a sugar motif selected from among those listed in the following non-limiting tables:

TABLE 3 Certain 3′-Wing Sugar Motifs Certain 3′-Wing Sugar Motifs AAAAA ABCBB BABCC BCBBA CBACC AAAAB ABCBC BACAA BCBBB CBBAA AAAAC ABCCA BACAB BCBBC CBBAB AAABA ABCCB BACAC BCBCA CBBAC AAABB ABCCC BACBA BCBCB CBBBA AAABC ACAAA BACBB BCBCC CBBBB AAACA ACAAB BACBC BCCAA CBBBC AAACB ACAAC BACCA BCCAB CBBCA AAACC ACABA BACCB BCCAC CBBCB AABAA ACABB BACCC BCCBA CBBCC AABAB ACABC BBAAA BCCBB CBCAA AABAC ACACA BBAAB BCCBC CBCAB AABBA ACACB BBAAC BCCCA CBCAC AABBB ACACC BBABA BCCCB CBCBA AABBC ACBAA BBABB BCCCC CBCBB AABCA ACBAB BBABC CAAAA CBCBC AABCB ACBAC BBACA CAAAB CBCCA AABCC ACBBA BBACB CAAAC CBCCB AACAA ACBBB BBACC CAABA CBCCC AACAB ACBBC BBBAA CAABB CCAAA AACAC ACBCA BBBAB CAABC CCAAB AACBA ACBCB BBBAC CAACA CCAAC AACBB ACBCC BBBBA CAACB CCABA AACBC ACCAA BBBBB CAACC CCABB AACCA ACCAB BBBBC CABAA CCABC AACCB ACCAC BBBCA CABAB CCACA AACCC ACCBA BBBCB CABAC CCACB ABAAA ACCBB BBBCC CABBA CCACC ABAAB ACCBC BBCAA CABBB CCBAA ABAAC ACCCA BBCAB CABBC CCBAB ABABA ACCCB BBCAC CABCA CCBAC ABABB ACCCC BBCBA CABCB CCBBA ABABC BAAAA BBCBB CABCC CCBBB ABACA BAAAB BBCBC CACAA CCBBC ABACB BAAAC BBCCA CACAB CCBCA ABACC BAABA BBCCB CACAC CCBCB ABBAA BAABB BBCCC CACBA CCBCC ABBAB BAABC BCAAA CACBB CCCAA ABBAC BAACA BCAAB CACBC CCCAB ABBBA BAACB BCAAC CACCA CCCAC ABBBB BAACC BCABA CACCB CCCBA ABBBC BABAA BCABB CACCC CCCBB ABBCA BABAB BCABC CBAAA CCCBC ABBCB BABAC BCACA CBAAB CCCCA ABBCC BABBA BCACB CBAAC CCCCB ABCAA BABBB BCACC CBABA CCCCC ABCAB BABBC BCBAA CBABB ABCAC BABCA BCBAB CBABC ABCBA BABCB BCBAC CBACA

TABLE 4 Certain 3′-Wing Sugar Motifs Certain 3′-Wing Sugar Motifs AAAAA BABC CBAB ABBB BAA AAAAB BACA CBAC BAAA BAB AAABA BACB CBBA BAAB BBA AAABB BACC CBBB BABA BBB AABAA BBAA CBBC BABB AA AABAB BBAB CBCA BBAA AB AABBA BBAC CBCB BBAB AC AABBB BBBA CBCC BBBA BA ABAAA BBBB CCAA BBBB BB ABAAB BBBC CCAB AAA BC ABABA BBCA CCAC AAB CA ABABB BBCB CCBA AAC CB ABBAA BBCC CCBB ABA CC ABBAB BCAA CCBC ABB AA ABBBA BCAB CCCA ABC AB ABBBB BCAC CCCB ACA BA BAAAA ABCB BCBA ACB BAAAB ABCC BCBB ACC BAABA ACAA BCBC BAA BAABB ACAB BCCA BAB BABAA ACAC BCCB BAC BABAB ACBA BCCC BBA BABBA ACBB CAAA BBB BABBB ACBC CAAB BBC BBAAA ACCA CAAC BCA BBAAB ACCB CABA BCB BBABA ACCC CABB BCC BBABB BAAA CABC CAA BBBAA BAAB CACA CAB BBBAB BAAC CACB CAC BBBBA BABA CACC CBA BBBBB BABB CBAA CBB AAAA AACC CCCC CBC AAAB ABAA AAAA CCA AAAC ABAB AAAB CCB AABA ABAC AABA CCC AABB ABBA AABB AAA AABC ABBB ABAA AAB AACA ABBC ABAB ABA AACB ABCA ABBA ABB

In certain embodiments, each A, each B, and each C located at the 5′-most 3′-wing region nucleoside is a modified nucleoside. For example, in certain embodiments the 3′-wing motif is selected from among ABB, BBB, and CBB, wherein the underlined nucleoside represents the 5′-most 3′-wing region nucleoside and wherein the underlined nucleoside is a modified nucleoside.

In certain embodiments, each A comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each A comprises a modified sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, ara-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each A comprises a bicyclic sugar moiety. In certain embodiments, each A comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises a modified nucleobase. In certain embodiments, each A comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne uridine nucleoside. In certain embodiments, each A comprises a 5′-substituted sugar moiety selected from among 5′-Me DNA, and 5′-(R)-Me DNA.

In certain embodiments, each B comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each B comprises a modified sugar moiety. In certain embodiments, each B comprises a 2′-substituted sugar moiety. In certain embodiments, each B comprises a 2′-subsituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each B comprises a bicyclic sugar moiety. In certain embodiments, each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each B comprises a modified nucleobase. In certain embodiments, each B comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne urindine nucleoside. In certain embodiments, each B comprises an HNA. In certain embodiments, each B comprises an F-HNA. In certain embodiments, each B comprises a 5′-substituted sugar moiety selected from among 5′-Me DNA, and 5′-(R)-Me DNA.

In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, ara-F, OCH₃ and O(CH₂)₂—OCH₃ and each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises O(CH₂)₂—OCH₃ and each B comprises cEt.

In certain embodiments, each C comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each C comprises a modified sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each C comprises a 5′-substituted sugar moiety. In certain embodiments, each C comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, each C comprises a bicyclic sugar moiety. In certain embodiments, each C comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each C comprises a modified nucleobase. In certain embodiments, each C comprises a modified nucleobase selected from among 2-thio-thymidine and 5-propyne uridine. In certain embodiments, each C comprises a 2-thio-thymidine nucleoside. In certain embodiments, each C comprises an HNA. In certain embodiments, each C comprises an F-HNA.

vi. Certain Central Regions (Gaps)

In certain embodiments, the gap of a gapmer consists of 6 to 20 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 15 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 12 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 or 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 or 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 or 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 11 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 12 linked nucleosides.

In certain embodiments, each nucleoside of the gap of a gapmer is a 2′-deoxynucleoside. In certain embodiments, the gap comprises one or more modified nucleosides. In certain embodiments, each nucleoside of the gap of a gapmer is a 2′-deoxynucleoside or is a modified nucleoside that is “DNA-like.” In such embodiments, “DNA-like” means that the nucleoside has similar characteristics to DNA, such that a duplex comprising the gapmer and an RNA molecule is capable of activating RNase H. For example, under certain conditions, 2′-(ara)-F have been shown to support RNase H activation, and thus is DNA-like. In certain embodiments, one or more nucleosides of the gap of a gapmer is not a 2′-deoxynucleoside and is not DNA-like. In certain such embodiments, the gapmer nonetheless supports RNase H activation (e.g., by virtue of the number or placement of the non-DNA nucleosides).

In certain embodiments, gaps comprise a stretch of unmodified 2′-deoxynucleoside interrupted by one or more modified nucleosides, thus resulting in three sub-regions (two stretches of one or more 2′-deoxynucleosides and a stretch of one or more interrupting modified nucleosides). In certain embodiments, no stretch of unmodified 2′-deoxynucleosides is longer than 5, 6, or 7 nucleosides. In certain embodiments, such short stretches is achieved by using short gap regions. In certain embodiments, short stretches are achieved by interrupting a longer gap region.

In certain embodiments, the gap comprises one or more modified nucleosides. In certain embodiments, the gap comprises one or more modified nucleosides selected from among cEt, FHNA, LNA, and 2-thio-thymidine. In certain embodiments, the gap comprises one modified nucleoside. In certain embodiments, the gap comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, the gap comprises two modified nucleosides. In certain embodiments, the gap comprises three modified nucleosides. In certain embodiments, the gap comprises four modified nucleosides. In certain embodiments, the gap comprises two or more modified nucleosides and each modified nucleoside is the same. In certain embodiments, the gap comprises two or more modified nucleosides and each modified nucleoside is different.

In certain embodiments, the gap comprises one or more modified linkages. In certain embodiments, the gap comprises one or more methyl phosphonate linkages. In certain embodiments the gap comprises two or more modified linkages. In certain embodiments, the gap comprises one or more modified linkages and one or more modified nucleosides. In certain embodiments, the gap comprises one modified linkage and one modified nucleoside. In certain embodiments, the gap comprises two modified linkages and two or more modified nucleosides.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DDDDXDDDDD; DDDDDXDDDDD; DDDXDDDDD; DDDDXDDDDDD; DDDDXDDDD; DDXDDDDDD; DDDXDDDDDD; DXDDDDDD; DDXDDDDDDD; DDXDDDDD; DDXDDDXDDD; DDDXDDDXDDD; DXDDDXDDD; DDXDDDXDD; DDXDDDDXDDD; DDXDDDDXDD; DXDDDDXDDD; DDDDXDDD; DDDXDDD; DXDDDDDDD; DDDDXXDDD; and DXXDXXDXX; wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DDDDDDDDD; DXDDDDDDD; DDXDDDDDD; DDDXDDDDD; DDDDXDDDD; DDDDDXDDD; DDDDDDXDD; DDDDDDDXD; DXXDDDDDD; DDDDDDXXD; DDXXDDDDD; DDDXXDDDD; DDDDXXDDD; DDDDDXXDD; DXDDDDDXD; DXDDDDXDD; DXDDDXDDD; DXDDXDDDD; DXDXDDDDD; DDXDDDDXD; DDXDDDXDD; DDXDDXDDD; DDXDXDDDD; DDDXDDDXD; DDDXDDXDD; DDDXDXDDD; DDDDXDDXD; DDDDXDXDD; and DDDDDXDXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DDDDXDDDD, DXDDDDDDD, DXXDDDDDD, DDXDDDDDD, DDDXDDDDD, DDDDXDDDD, DDDDDXDDD, DDDDDDXDD, and DDDDDDDXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DDDDDDDD, DXDDDDDD, DDXDDDDD, DDDXDDDD, DDDDXDDD, DDDDDXDD, DDDDDDXD, DXDDDDXD, DXDDDXDD, DXDDXDDD, DXDXDDDD, DXXDDDDD, DDXXDDDD, DDXDXDDD, DDXDDXDD, DXDDDDXD, DDDXXDDD, DDDXDXDD, DDDXDDXD, DDDDXXDD, DDDDXDXD, and DDDDDXXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DXDDDDD, DDXDDDD, DDDXDDD, DDDDXDD, DDDDDXD, DXDDDXD, DXDDXDD, DXDXDDD, DXXDDDD, DDXXDDD, DDXDXDD, DDXDDXD, DDDXXDD, DDDXDXD, and DDDDXXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DXDDDD, DDXDDD, DDDXDD, DDDDXD, DXXDDD, DXDXDD, DXDDXD, DDXXDD, DDXDXD, and DDDXXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, the gap comprises a nucleoside motif selected from among the following: DXDDDD, DDXDDD, DDDXDD, DDDDXD, DXDDDDD, DDXDDDD, DDDXDDD, DDDDXDD, DDDDDXD, DXDDDDDD, DDXDDDDD, DDDXDDDD, DDDDXDDD, DDDDDXDD, DDDDDDXD, DXDDDDDDD; DDXDDDDDD, DDDXDDDDD, DDDDXDDDD, DDDDDXDDD, DDDDDDXDD, DDDDDDDXD, DXDDDDDDDD, DDXDDDDDDD, DDDXDDDDDD, DDDDXDDDDD, DDDDDXDDDD, DDDDDDXDDD, DDDDDDDXDD, and DDDDDDDDXD, wherein each D is an unmodified deoxynucleoside; and each X is a modified nucleoside or a substituted sugar moiety.

In certain embodiments, each X comprises an unmodified 2′-deoxyfuranose sugar moiety. In certain embodiments, each X comprises a modified sugar moiety. In certain embodiments, each X comprises a 2′-substituted sugar moiety. In certain embodiments, each X comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each X comprises a 5′-substituted sugar moiety. In certain embodiments, each X comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, each X comprises a bicyclic sugar moiety. In certain embodiments, each X comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each X comprises a modified nucleobase. In certain embodiments, each X comprises a modified nucleobase selected from among 2-thio-thymidine and 5-propyne uridine. In certain embodiments, each X comprises a 2-thio-thymidine nucleoside. In certain embodiments, each X comprises an HNA. In certain embodiments, each C comprises an F-HNA. In certain embodiments, X represents the location of a single differentiating nucleobase.

vii. Certain Gapmer Motifs

In certain embodiments, a gapmer comprises a 5′-wing, a gap, and a 3′ wing, wherein the 5′-wing, gap, and 3′ wing are independently selected from among those discussed above. For example, in certain embodiments, a gapmer has a 5′-wing, a gap, and a 3′-wing having features selected from among any of those listed in the tables above and any 5′-wing may be paired with any gap and any 3′-wing. For example, in certain embodiments, a 5′-wing may comprise AAABB, a 3′-wing may comprise BBA, and the gap may comprise DDDDDDD. For example, in certain embodiments, a gapmer has a 5′-wing, a gap, and a 3′-wing having features selected from among those listed in the following non-limiting table, wherein each motif is represented as (5′-wing)-(gap)-(3′-wing), wherein each number represents the number of linked nucleosides in each portion of the motif, for example, a 5-10-5 motif would have a 5′-wing comprising 5 nucleosides, a gap comprising 10 nucleosides, and a 3′-wing comprising 5 nucleosides:

TABLE 5 Certain Gapmer Sugar Motifs Certain Gapmer Sugar Motifs 2-10-2 3-10-2 4-10-2 5-10-2 2-10-3 3-10-3 4-10-3 5-10-3 2-10-4 3-10-4 4-10-4 5-10-4 2-10-5 3-10-5 4-10-5 5-10-5 2-9-2 3-9-2 4-9-2 5-9-2 2-9-3 3-9-3 4-9-3 5-9-3 2-9-4 3-9-4 4-9-4 5-9-4 2-9-5 3-9-5 4-9-5 5-9-5 2-11-2 3-11-2 4-11-2 5-11-2 2-11-3 3-11-3 4-11-3 5-11-3 2-11-4 3-11-4 4-11-4 5-11-4 2-11-5 3-11-5 4-11-5 5-11-5 2-8-2 3-8-2 4-8-2 5-8-2 2-8-3 3-8-3 4-8-3 5-8-3 2-8-4 3-8-4 4-8-4 5-8-4 2-8-5 3-8-5 4-8-5 5-8-5

In certain embodiments, a gapmer comprises a 5′-wing, a gap, and a 3′ wing, wherein the 5′-wing, gap, and 3′ wing are independently selected from among those discussed above. For example, in certain embodiments, a gapmer has a 5′-wing, a gap, and a 3′-wing having features selected from among those listed in the following non-limiting tables:

TABLE 6 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region ADDA DDDDDD ABB ABBA DDDADDDD ABAA AAAAAAA DDDDDDDDDDD AAA AAAAABB DDDDDDDD BBAAAAA ABB DDDDADDDD ABB ABB DDDDBDDDD BBA ABB DDDDDDDDD BBA AABAA DDDDDDDDD AABAA ABB DDDDDD AABAA AAABAA DDDDDDDDD AAABAA AAABAA DDDDDDDDD AAB ABAB DDDDDDDDD ABAB AAABB DDDDDDD BBA ABADB DDDDDDD BBA ABA DBDDDDDDD BBA ABA DADDDDDDD BBA ABAB DDDDDDDD BBA AA DDDDDDDD BBBBBBBB ABB DDDDDD ABADB AAAAB DDDDDDD BAAAA ABBB DDDDDDDDD AB AB DDDDDDDDD BBBA ABBB DDDDDDDDD BBBA AB DDDDDDDD ABA ABB DDDDWDDDD BBA AAABB DDDWDDD BBAAA ABB DDDDWWDDD BBA ABADB DDDDDDD BBA ABBDC DDDDDDD BBA ABBDDC DDDDDD BBA ABBDCC DDDDDD BBA ABB DWWDWWDWW BBA ABB DWDDDDDDD BBA ABB DDWDDDDDD BBA ABB DWWDDDDDD BBA AAABB DDWDDDDDD AA BB DDWDWDDDD BBABBBB ABB DDDD(^(N)D)DDDD BBA AAABB DDD(^(N)D)DDD BBAAA ABB DDDD(^(N)D)(^(N)D)DDD BBA ABB D(^(N)D)(^(N)D)D(^(N)D)(^(N)D) BBA D(^(N)D)(^(N)D) ABB D(^(N)D)DDDDDDD BBA ABB DD(^(N)D)DDDDDD BBA ABB D(^(N)D)(^(N)D)DDDDDD BBA AAABB DD(^(N)D)DDDDDD AA BB DD(^(N)D)D(^(N)D)DDDD BBABBBB ABAB DDDDDDDDD BABA

TABLE 7 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region ABBW DDDDDDDD BBA ABB DWDDDDDDD BBA ABB DDWDDDDDD BBA ABB DDDWDDDDD BBA ABB DDDDWDDDD BBA ABB DDDDDWDDD BBA ABB DDDDDDWDD BBA ABB DDDDDDDWD BBA ABB DDDDDDDD WBBA ABBWW DDDDDDD BBA ABB DWWDDDDDD BBA ABB DDWWDDDDD BBA ABB DDDWWDDDD BBA ABB DDDDWWDDD BBA ABB DDDDDWWDD BBA ABB DDDDDDWWD BBA ABB DDDDDDD WWBBA ABBW DDDDDDD WBBA ABBW DDDDDDWD BBA ABBW DDDDDWDD BBA ABBW DDDDWDDD BBA ABBW DDDWDDDD BBA ABBW DDWDDDDD BBA ABBW DWDDDDDD BBA ABB DWDDDDDD WBBA ABB DWDDDDDWD BBA ABB DWDDDDWDD BBA ABB DWDDDWDDD BBA ABB DWDDWDDDD BBA ABB DWDWDDDDD BBA ABB DDWDDDDD WBBA ABB DDWDDDDWD BBA ABB DDWDDDWDD BBA ABB DDWDDWDDD BBA ABB DDWDWDDDD BBA ABB DDWWDDDDD BBA ABB DDDWDDDD WBBA ABB DDDWDDDWD BBA ABB DDDWDDWDD BBA ABB DDDWDWDDD BBA ABB DDDWWDDDD BBA ABB DDDDWDDD WBBA ABB DDDDWDDWD BBA ABB DDDDWDWDD BBA ABB DDDDWWDDD BBA ABB DDDDDWDD WBBA ABB DDDDDWDWD BBA ABB DDDDDWWDD BBA ABB DDDDDDWD WBBA

TABLE 8 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region ABBB DDDDDDDD BBA ABB DBDDDDDDD BBA ABB DDBDDDDDD BBA ABB DDDBDDDDD BBA ABB DDDDBDDDD BBA ABB DDDDDBDDD BBA ABB DDDDDDBDD BBA ABB DDDDDDDBD BBA ABB DDDDDDDD BBBA ABBBB DDDDDDD BBA ABB DBBDDDDDD BBA ABB DDBBDDDDD BBA ABB DDDBBDDDD BBA ABB DDDDBBDDD BBA ABB DDDDDBBDD BBA ABB DDDDDDBBD BBA ABB DDDDDDD BBBBA ABBB DDDDDDD BBBA ABB DDDDDDBD BBA ABBB DDDDDBDD BBA ABBB DDDDBDDD BBA ABBB DDDBDDDD BBA ABBB DDBDDDDD BBA ABBB DBDDDDDD BBA ABB DBDDDDDD BBBA ABB DBDDDDDBD BBA ABB DBDDDDBDD BBA ABB DBDDDBDDD BBA ABB DBDDBDDDD BBA ABB DBDBDDDDD BBA ABB DDBDDDDD BBBA ABB DDBDDDDBD BBA ABB DDBDDDBDD BBA ABB DDBDDBDDD BBA ABB DDBDBDDDD BBA ABB DDBBDDDDD BBA ABB DDDBDDDD BBBA ABB DDDBDDDBD BBA ABB DDDBDDBDD BBA ABB DDDBDBDDD BBA ABB DDDBBDDDD BBA ABB DDDDBDDD BBBA ABB DDDDBDDBD BBA ABB DDDDBDBDD BBA ABB DDDDBBDDD BBA ABB DDDDDBDD BBBA ABB DDDDDBDBD BBA ABB DDDDDBBDD BBA ABB DDDDDDBD BBBA

TABLE 9 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region ABB DDDDDDDDD BBA AB DBDDDDDDDD BBA AB DDBDDDDDDD BBA AB DDDBDDDDDD BBA AB DDDDBDDDDD BBA AB DDDDDBDDDD BBA AB DDDDDDBDDD BBA AB DDDDDDDBDD BBA AB DDDDDDDDBD BBA AB DDDDDDDDD BBBA ABBB DDDDDDDD BBA AB DBBDDDDDDD BBA AB DDBBDDDDDD BBA AB DDDBBDDDDD BBA AB DDDDBBDDDD BBA AB DDDDDBBDDD BBA AB DDDDDDBBDD BBA AB DDDDDDDBBD BBA AB DDDDDDDD BBBBA ABBBB DDDDDDD BBA AB DBBBDDDDDD BBA AB DDBBBDDDDD BBA AB DDDBBBDDDD BBA AB DDDDBBBDDD BBA AB DDDDDBBBDD BBA AB DDDDDDBBBD BBA AB DDDDDDD BBBBBA AB DDDDDDDDD BBBA AB DDDDDDDBD BBBA AB DDDDDBDD BBBA AB DDDDBDDD BBBA AB DDDBDDDD BBBA AB DDBDDDDD BBBA AB DBDDDDDD BBBA AB DDDDDBD BBBBA AB DDDDBDD BBBBA AB DDDBDDD BBBBA AB DDBDDDD BBBBA AB DBDDDDD BBBBA AB DDDDBD BBBBBA AB DDDBDD BBBBBA AB DDBDDD BBBBBA AB DBDDDD BBBBBA

TABLE 10 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region AAAAAA DDDDDDD BABA AAAAAB DDDDDDD BABA AAAABA DDDDDDD BABA AAABAA DDDDDDD BABA AABAAA DDDDDDD BABA ABAAAA DDDDDDD BABA BAAAAA DDDDDDD BABA ABAAAB DDDDDDD BABA ABAABA DDDDDDD BABA ABABAA DDDDDDD BABA ABBAAA DDDDDDD BABA AABAAB DDDDDDD BABA AABABA DDDDDDD BABA AABBAA DDDDDDD BABA AAABAB DDDDDDD BABA AAABBA DDDDDDD BABA AAAABB DDDDDDD BABA BAAAAB DDDDDDD BABA BAAABA DDDDDDD BABA BAABAA DDDDDDD BABA BABAAA DDDDDDD BABA BBAAAA DDDDDDD BABA BBBAAA DDDDDDD BABA BBABAA DDDDDDD BABA BBAABA DDDDDDD BABA BBAAAB DDDDDDD BABA ABABAB DDDDDDD BABA BBBBAA DDDDDDD BABA BBBABA DDDDDDD BABA BBBAAB DDDDDDD BABA BBBBBA DDDDDDD BABA BBBBAB DDDDDDD BABA AAABBB DDDDDDD BABA AABABB DDDDDDD BABA ABAABB DDDDDDD BABA BAAABB DDDDDDD BABA AABBBB DDDDDDD BABA ABABBB DDDDDDD BABA BAABBB DDDDDDD BABA ABBBBB DDDDDDD BABA BABBBB DDDDDDD BABA BBBBBB DDDDDDD BABA

TABLE 11 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region AAAAA DDDDDDD AAAAA AAAAB DDDDDDD AAAAA AAABA DDDDDDD AAAAA AAABB DDDDDDD AAAAA AABAA DDDDDDD AAAAA AABAB DDDDDDD AAAAA AABBA DDDDDDD AAAAA AABBB DDDDDDD AAAAA ABAAA DDDDDDD AAAAA ABAAB DDDDDDD AAAAA ABABA DDDDDDD AAAAA ABABB DDDDDDD AAAAA ABBAA DDDDDDD AAAAA ABBAB DDDDDDD AAAAA ABBBA DDDDDDD AAAAA ABBBB DDDDDDD AAAAA BAAAA DDDDDDD AAAAA BAAAB DDDDDDD AAAAA BAABA DDDDDDD AAAAA BAABB DDDDDDD AAAAA BABAA DDDDDDD AAAAA BABAB DDDDDDD AAAAA BABBA DDDDDDD AAAAA BABBB DDDDDDD AAAAA BBAAA DDDDDDD AAAAA BBAAB DDDDDDD AAAAA BBABA DDDDDDD AAAAA BBABB DDDDDDD AAAAA BBBAA DDDDDDD AAAAA BBBAB DDDDDDD AAAAA BBBBA DDDDDDD AAAAA BBBBB DDDDDDD AAAAA AAAAA DDDDDDD BAAAA AAAAB DDDDDDD BAAAA AAABA DDDDDDD BAAAA AAABB DDDDDDD BAAAA AABAA DDDDDDD BAAAA AABAB DDDDDDD BAAAA AABBA DDDDDDD BAAAA AABBB DDDDDDD BAAAA ABAAA DDDDDDD BAAAA ABAAB DDDDDDD BAAAA ABABA DDDDDDD BAAAA ABABB DDDDDDD BAAAA ABBAA DDDDDDD BAAAA ABBAB DDDDDDD BAAAA ABBBA DDDDDDD BAAAA ABBBB DDDDDDD BAAAA BAAAA DDDDDDD BAAAA BAAAB DDDDDDD BAAAA BAABA DDDDDDD BAAAA BAABB DDDDDDD BAAAA BABAA DDDDDDD BAAAA BABAB DDDDDDD BAAAA BABBA DDDDDDD BAAAA BABBB DDDDDDD BAAAA BBAAA DDDDDDD BAAAA BBAAB DDDDDDD BAAAA BBABA DDDDDDD BAAAA BBABB DDDDDDD BAAAA BBBAA DDDDDDD BAAAA BBBAB DDDDDDD BAAAA BBBBA DDDDDDD BAAAA BBBBB DDDDDDD BAAAA AAAAA DDDDDDD BBAAA AAAAB DDDDDDD BBAAA AAABA DDDDDDD BBAAA AAABB DDDDDDD BBAAA AABAA DDDDDDD BBAAA AABAB DDDDDDD BBAAA AABBA DDDDDDD BBAAA AABBB DDDDDDD BBAAA ABAAA DDDDDDD BBAAA ABAAB DDDDDDD BBAAA ABABA DDDDDDD BBAAA ABABB DDDDDDD BBAAA ABBAA DDDDDDD BBAAA ABBAB DDDDDDD BBAAA ABBBA DDDDDDD BBAAA ABBBB DDDDDDD BBAAA BAAAA DDDDDDD BBAAA BAAAB DDDDDDD BBAAA BAABA DDDDDDD BBAAA BAABB DDDDDDD BBAAA BABAA DDDDDDD BBAAA BABAB DDDDDDD BBAAA BABBA DDDDDDD BBAAA BABBB DDDDDDD BBAAA BBAAA DDDDDDD BBAAA BBAAB DDDDDDD BBAAA BBABA DDDDDDD BBAAA BBABB DDDDDDD BBAAA BBBAA DDDDDDD BBAAA BBBAB DDDDDDD BBAAA BBBBA DDDDDDD BBAAA BBBBB DDDDDDD BBAAA AAAAA DDDDDDD BBBAA AAAAB DDDDDDD BBBAA AAABA DDDDDDD BBBAA AAABB DDDDDDD BBBAA AABAA DDDDDDD BBBAA AABAB DDDDDDD BBBAA AABBA DDDDDDD BBBAA AABBB DDDDDDD BBBAA ABAAA DDDDDDD BBBAA ABAAB DDDDDDD BBBAA ABABA DDDDDDD BBBAA ABABB DDDDDDD BBBAA ABBAA DDDDDDD BBBAA ABBAB DDDDDDD BBBAA ABBBA DDDDDDD BBBAA ABBBB DDDDDDD BBBAA BAAAA DDDDDDD BBBAA BAAAB DDDDDDD BBBAA BAABA DDDDDDD BBBAA BAABB DDDDDDD BBBAA BABAA DDDDDDD BBBAA BABAB DDDDDDD BBBAA BABBA DDDDDDD BBBAA BABBB DDDDDDD BBBAA BBAAA DDDDDDD BBBAA BBAAB DDDDDDD BBBAA BBABA DDDDDDD BBBAA BBABB DDDDDDD BBBAA BBBAA DDDDDDD BBBAA BBBAB DDDDDDD BBBAA BBBBA DDDDDDD BBBAA BBBBB DDDDDDD BBBAA AAAAA DDDDDDD BBBBA AAAAB DDDDDDD BBBBA AAABA DDDDDDD BBBBA AAABB DDDDDDD BBBBA AABAA DDDDDDD BBBBA AABAB DDDDDDD BBBBA AABBA DDDDDDD BBBBA AABBB DDDDDDD BBBBA ABAAA DDDDDDD BBBBA ABAAB DDDDDDD BBBBA ABABA DDDDDDD BBBBA ABABB DDDDDDD BBBBA ABBAA DDDDDDD BBBBA ABBAB DDDDDDD BBBBA ABBBA DDDDDDD BBBBA ABBBB DDDDDDD BBBBA BAAAA DDDDDDD BBBBA BAAAB DDDDDDD BBBBA BAABA DDDDDDD BBBBA BAABB DDDDDDD BBBBA BABAA DDDDDDD BBBBA BABAB DDDDDDD BBBBA BABBA DDDDDDD BBBBA BABBB DDDDDDD BBBBA BBAAA DDDDDDD BBBBA BBAAB DDDDDDD BBBBA BBABA DDDDDDD BBBBA BBABB DDDDDDD BBBBA BBBAA DDDDDDD BBBBA BBBAB DDDDDDD BBBBA BBBBA DDDDDDD BBBBA BBBBB DDDDDDD BBBBA AAAAA DDDDDDD BBBBB AAAAB DDDDDDD BBBBB AAABA DDDDDDD BBBBB AAABB DDDDDDD BBBBB AABAA DDDDDDD BBBBB AABAB DDDDDDD BBBBB AABBA DDDDDDD BBBBB AABBB DDDDDDD BBBBB ABAAA DDDDDDD BBBBB ABAAB DDDDDDD BBBBB ABABA DDDDDDD BBBBB ABABB DDDDDDD BBBBB ABBAA DDDDDDD BBBBB ABBAB DDDDDDD BBBBB ABBBA DDDDDDD BBBBB ABBBB DDDDDDD BBBBB BAAAA DDDDDDD BBBBB BAAAB DDDDDDD BBBBB BAABA DDDDDDD BBBBB BAABB DDDDDDD BBBBB BABAA DDDDDDD BBBBB BABAB DDDDDDD BBBBB BABBA DDDDDDD BBBBB BABBB DDDDDDD BBBBB BBAAA DDDDDDD BBBBB BBAAB DDDDDDD BBBBB BBABA DDDDDDD BBBBB BBABB DDDDDDD BBBBB BBBAA DDDDDDD BBBBB BBBAB DDDDDDD BBBBB BBBBA DDDDDDD BBBBB BBBBB DDDDDDD BBBBB

TABLE 12 Certain Gapmer Nucleoside Motifs 5′-wing region Central gap region 3′-wing region AAAW DDDDDDDD BBA AABW DDDDDDDD BBA ABAW DDDDDDDD BBA ABBW DDDDDDDD BBA BAAW DDDDDDDD BBA BABW DDDDDDDD BBA BBAW DDDDDDDD BBA BBBW DDDDDDDD BBA ABB DDDDDDDD WAAA ABB DDDDDDDD WAAB ABB DDDDDDDD WABA ABB DDDDDDDD WABB ABB DDDDDDDD WBAA ABB DDDDDDDD WBAB ABB DDDDDDDD WBBA ABB DDDDDDDD WBBB AAAWW DDDDDDD BBA AABWW DDDDDDD BBA ABAWW DDDDDDD BBA ABBWW DDDDDDD BBA BAAWW DDDDDDD BBA BABWW DDDDDDD BBA BBAWW DDDDDDD BBA BBBWW DDDDDDD BBA ABB DDDDDDD WWAAA ABB DDDDDDD WWAAB ABB DDDDDDD WWABA ABB DDDDDDD WWABB ABB DDDDDDD WWBAA ABB DDDDDDD WWBAB ABB DDDDDDD WWBBA ABB DDDDDDD WWBBB AAAAW DDDDDDD BBA AAABW DDDDDDD BBA AABAW DDDDDDD BBA AABBW DDDDDDD BBA ABAAW DDDDDDD BBA ABABW DDDDDDD BBA ABBAW DDDDDDD BBA ABBBW DDDDDDD BBA BAAAW DDDDDDD BBA BAABW DDDDDDD BBA BABAW DDDDDDD BBA BABBW DDDDDDD BBA BBAAW DDDDDDD BBA BBABW DDDDDDD BBA BBBAW DDDDDDD BBA BBBBW DDDDDDD WAAAA ABB DDDDDDD WAAAB ABB DDDDDDD WAABA ABB DDDDDDD WAABB ABB DDDDDDD WABAA ABB DDDDDDD WABAB ABB DDDDDDD WABBA ABB DDDDDDD WABBB ABB DDDDDDD WBAAA ABB DDDDDDD WBAAB ABB DDDDDDD WBABA ABB DDDDDDD WBABB ABB DDDDDDD WBBAA ABB DDDDDDD WBBAB ABB DDDDDDD WBBBA ABB DDDDDDD WBBBB wherein each A is a modified nucleoside of a first type, each B is a modified nucleoside of a second type and each W is a modified nucleoside or nucleobase of either the first type, the second type or a third type, each D is a nucleoside comprising an unmodified 2′deoxy sugar moiety and unmodified nucleobase, and^(N)D is modified nucleoside comprising a modified nucleobase and an unmodified 2′deoxy sugar moiety.

In certain embodiments, each A comprises a modified sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, ara-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each A comprises a bicyclic sugar moiety. In certain embodiments, each A comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises a modified nucleobase. In certain embodiments, each A comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne uridine nucleoside. In certain embodiments, each A comprises an HNA. In certain embodiments, each A comprises an F-HNA. In certain embodiments, each A comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me.

In certain embodiments, each B comprises a modified sugar moiety. In certain embodiments, each B comprises a 2′-substituted sugar moiety. In certain embodiments, each B comprises a 2′-subsituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each B comprises a bicyclic sugar moiety. In certain embodiments, each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each B comprises a modified nucleobase. In certain embodiments, each B comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne urindine nucleoside. In certain embodiments, each B comprises an HNA. In certain embodiments, each B comprises an F-HNA. In certain embodiments, each B comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me.

In certain embodiments, each C comprises a modified sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety. In certain embodiments, each C comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each C comprises a 5′-substituted sugar moiety. In certain embodiments, each C comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, each C comprises a bicyclic sugar moiety. In certain embodiments, each C comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each C comprises a modified nucleobase. In certain embodiments, each C comprises a modified nucleobase selected from among 2-thio-thymidine and 5-propyne uridine. In certain embodiments, each C comprises a 2-thio-thymidine nucleoside. In certain embodiments, each C comprises an HNA. In certain embodiments, each C comprises an F-HNA.

In certain embodiments, each W comprises a modified sugar moiety. In certain embodiments, each W comprises a 2′-substituted sugar moiety. In certain embodiments, each W comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each W comprises a 5′-substituted sugar moiety. In certain embodiments, each W comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, each W comprises a bicyclic sugar moiety. In certain embodiments, each W comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each W comprises a sugar surrogate. In certain embodiments, each W comprises a sugar surrogate selected from among HNA and F-HNA. In certain embodiments, each W comprises a 2-thio-thymidine nucleoside.

In certain embodiments, at least one of A or B comprises a bicyclic sugar moiety, and the other comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-substituted sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-MOE sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-F sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-F sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-F sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-F sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-MOE sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-F sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-F sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-F sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-F sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, at least one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-substituted sugar moiety and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and C comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and C comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and C comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and C comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar HNA surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, at least two of A, B or W comprises a 2′-substituted sugar moiety, and the other comprises a bicyclic sugar moiety. In certain embodiments, at least two of A, B or W comprises a bicyclic sugar moiety, and the other comprises a 2′-substituted sugar moiety. In certain embodiments, a gapmer has a sugar motif other than: E-K-K-(D)₉-K-K-E; E-E-E-E-K-(D)₉-E-E-E-E-E; E-K—K-K-(D)₉-K—K-K-E; K-E-E-K-(D)₉-K-E-E-K; K-D-D-K-(D)₉-K-D-D-K; K-E-K-E-K-(D)₉-K-E-K-E-K; K-D-K-D-K-(D)₉-K-D-K-D-K; E-K-E-K-(D)₉-K-E-K-E; E-E-E-E-E-K-(D)₈-E-E-E-E-E; or E-K-E-K-E-(D)₉-E-K-E-K-E, E-E-E-K-K-(D)₇-E-E-K, E-K-E-K—K-K-(D)₇-K-E-K-E, E-K-E-K-E-K-(D)₇-K-E-K-E, wherein K is a nucleoside comprising a cEt sugar moiety and E is a nucleoside comprising a 2′-MOE sugar moiety.

In certain embodiments a gapmer comprises a A-(D)₄-A-(D)₄-A-(D)₄-AA motif. In certain embodiments a gapmer comprises a B-(D)₄-A-(D)₄-A-(D)₄-AA motif. In certain embodiments a gapmer comprises a A-(D)₄-B-(D)₄-A-(D)₄-AA motif. In certain embodiments a gapmer comprises a A-(D)₄-A-(D)₄-B-(D)₄-AA motif. In certain embodiments a gapmer comprises a A-(D)₄-A-(D)₄-A-(D)₄-BA motif. In certain embodiments a gapmer comprises a A-(D)₄-A-(D)₄-A-(D)₄-BB motif. In certain embodiments a gapmer comprises a K-(D)₄-K-(D)₄-K-(D)₄-K-E motif.

viii. Certain Internucleoside Linkage Motifs

In certain embodiments, oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. In certain embodiments, internucleoside linkages are arranged in a gapped motif, as described above for nucleoside motif. In such embodiments, the internucleoside linkages in each of two wing regions are different from the internucleoside linkages in the gap region. In certain embodiments the internucleoside linkages in the wings are phosphodiester and the internucleoside linkages in the gap are phosphorothioate. The nucleoside motif is independently selected, so such oligonucleotides having a gapped internucleoside linkage motif may or may not have a gapped nucleoside motif and if it does have a gapped nucleoside motif, the wing and gap lengths may or may not be the same.

In certain embodiments, oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides of the present invention comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.

In certain embodiments, the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.

In certain embodiments, oligonucleotides comprise one or more methylphosponate linkages. In certain embodiments, oligonucleotides having a gapmer nucleoside motif comprise a linkage motif comprising all phosphorothioate linkages except for one or two methylphosponate linkages. In certain embodiments, one methylphosponate linkage is in the central gap of an oligonucleotide having a gapmer nucleoside motif.

ix. Certain Modification Motifs

Modification motifs define oligonucleotides by nucleoside motif (sugar motif and nucleobase motif) and linkage motif. For example, certain oligonucleotides have the following modification motif:

A_(s)A_(s)A_(s)D_(s)D_(s)D_(s)D_(s)(^(N)D)_(s)D_(s)D_(s)D_(s)D_(s)B_(s)B_(s)B;

wherein each A is a modified nucleoside comprising a 2′-substituted sugar moiety; each D is an unmodified 2′-deoxynucleoside; each B is a modified nucleoside comprising a bicyclic sugar moiety; ^(N)D is a modified nucleoside comprising a modified nucleobase; and s is a phosphorothioate internucleoside linkage. Thus, the sugar motif is a gapmer motif. The nucleobase modification motif is a single modified nucleobase at 8^(th) nucleoside from the 5′-end. Combining the sugar motif and the nucleobase modification motif, the nucleoside motif is an interrupted gapmer where the gap of the sugar modified gapmer is interrupted by a nucleoside comprising a modified nucleobase. The linkage motif is uniform phosphorothioate. The following non-limiting Table further illustrates certain modification motifs:

TABLE 13 Certain Modification Motifs 5′-wing region Central gap region 3′-wing region B_(s)B_(s) _(s)D_(s)D_(s)D_(s)D_(s)D_(s)D_(s)D_(s)D_(s)D_(s) A_(s)A_(s)A_(s)A_(s)A_(s)A_(s)A_(s)A AsBsBs DsDsDsDsDsDsDsDsDs BsBsA AsBsBs DsDsDsDs(^(N)D)sDsDsDsDs BsBsA AsBsBs DsDsDsDsAsDsDsDsDs BsBsA AsBsBs DsDsDsDsBsDsDsDsDs BsBsA AsBsBs DsDsDsDsWsDsDsDsDs BsBsA AsBsBsBs DsDsDsDsDsDsDsDsDs BsBsAsBsB AsBsBs DsDsDsDsDsDsDsDsDs BsBsAsBsB BsBsAsBsBs DsDsDsDsDsDsDsDsDs BsBsA AsBsBs DsDsDsDsDsDsDsDsDs BsBsAsBsBsBsB AsAsBsAsAs DsDsDsDsDsDsDsDsDs BsBsA AsAsAsBsAsAs DsDsDsDsDsDsDsDsDs BsBsA AsAsBsAsAs DsDsDsDsDsDsDsDsDs AsAsBsAsA AsAsAsBsAsAs DsDsDsDsDsDsDsDsDs AsAsBsAsAsA AsAsAsAsBsAsAs DsDsDsDsDsDsDsDsDs BsBsA AsBsAsBs DsDsDsDsDsDsDsDsDs BsAsBsA AsBsAsBs DsDsDsDsDsDsDsDsDs AsAsBsAsAs AsBsBs DsDsDsDsDsDsDsDsDs BsAsBsA BsBsAsBsBsBsB DsDsDsDsDsDsDsDsDs BsAsBsA AsAsAsAsAs DsDsDsDsDsDsDsDsDs AsAsAsAsA AsAsAsAsAs DsDsDsDsDsDsDs AsAsAsAsA AsAsAsAsAs DsDsDsDsDsDsDsDsDs BsBsAsBsBsBsB AsAsAsBsBs DsDsDsDsDsDsDs BsBsA AsBsAsBs DsDsDsDsDsDsDsDs BsBsA AsBsAsBs DsDsDsDsDsDsDs AsAsAsBsBs AsAsAsAsBs DsDsDsDsDsDsDs BsAsAsAsA BsBs DsDsDsDsDsDsDsDs AsA AsAs DsDsDsDsDsDsDs AsAsAsAsAsAsAsA AsAsAs DsDsDsDsDsDsDs AsAsAsAsAsAsA AsAsAs DsDsDsDsDsDsDs AsAsAsAsAsA AsBs DsDsDsDsDsDsDs BsBsBsA AsBsBsBs DsDsDsDsDsDsDsDsDs BsA AsBs DsDsDsDsDsDsDsDsDs BsBsBsA AsAsAsBsBs DsDsDs(^(N)D)sDsDsDs BsBsAsAsA AsAsAsBsBs DsDsDsAsDsDsDs BsBsAsAsA AsAsAsBsBs DsDsDsBsDsDsDs BsBsAsAsA AsAsAsAsBs DsDsDsDsDsDsDs BsAsAsAsA AsAsBsBsBs DsDsDsDsDsDsDs BsBsBsAsA AsAsAsAsBs DsDsDsDsDsDsDs AsAsAsAsAs AsAsAsBsBs DsDsDsDsDsDsDs AsAsAsAsAs AsAsBsBsBs DsDsDsDsDsDsDs AsAsAsAsAs AsAsAsAsAs DsDsDsDsDsDsDs BsAsAsAsAs AsAsAsAsAs DsDsDsDsDsDsDs BsBsAsAsAs AsAsAsAsAs DsDsDsDsDsDsDs BsBsBsAsAs AsBsBs DsDsDsDs(^(N)D)s(^(N)D)sDsDsDs BsBsA AsBsBs Ds(^(N)D)s(^(N)D)sDs(^(N)D)s(^(N)D)sDs(^(N)D)s(^(N)D)s BsBsA AsBsBs Ds(^(N)D)sDsDsDsDsDsDsDs BsBsA AsBsBs DsDs(^(N)D)sDsDsDsDsDsDs BsBsA AsBsBs Ds(^(N)D)s(^(N)D)sDsDsDsDsDsDs BsBsA AsBsBs DsDs(D)zDsDsDsDsDsDs BsBsA AsBsBs Ds(D)zDsDsDsDsDsDsDs BsBsA AsBsBs (D)zDsDsDsDsDsDsDsDs BsBsA AsBsBs DsDsAsDsDsDsDsDsDs BsBsA AsBsBs DsDsBsDsDsDsDsDsDs BsBsA AsBsBs AsDsDsDsDsDsDsDsDs BsBsA AsBsBs BsDsDsDsDsDsDsDsDs BsBsA AsBsAsBs DsDs(D)zDsDsDsDsDsDs BsBsBsAsAs AsAsAsBsBs DsDs(^(N)D)sDsDsDsDsDsDs AsA AsBsBsBs Ds(D)zDsDsDsDsDsDsDs AsAsAsBsBs AsBsBs DsDsDsDsDsDsDsDs(D)z BsBsA AsAsBsBsBs DsDsDsAsDsDsDs BsBsBsAsA AsAsBsBsBs DsDsDsBsDsDsDs BsBsBsAsA AsBsAsBs DsDsDsAsDsDsDs BsBsAsBsBsBsB AsBsBsBs DsDsDsDs(D)zDsDsDsDs BsA AsAsBsBsBs DsDsAsAsDsDsDs BsBsA AsBsBs DsDsDsDs(D)zDsDsDsDs BsBsBsA BsBs DsDs(^(N)D)sDs(^(N)D)sDsDsDsDs BsBsAsBsBsBsB wherein each A and B are nucleosides comprising differently modified sugar moieties, each D is a nucleoside comprising an unmodified 2′deoxy sugar moiety, each W is a modified nucleoside of either the first type, the second type or a third type, each ^(N)D is a modified nucleoside comprising a modified nucleobase, s is a phosphorothioate internucleoside linkage, and z is a non-phosphorothioate internucleoside linkage.

In certain embodiments, each A comprises a modified sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety. In certain embodiments, each A comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each A comprises a bicyclic sugar moiety. In certain embodiments, each A comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each A comprises a modified nucleobase. In certain embodiments, each A comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne uridine nucleoside. In certain embodiments, each B comprises a modified sugar moiety. In certain embodiments, each B comprises a 2′-substituted sugar moiety. In certain embodiments, each B comprises a 2′-subsituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each B comprises a bicyclic sugar moiety. In certain embodiments, each B comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each B comprises a modified nucleobase. In certain embodiments, each B comprises a modified nucleobase selected from among 2-thio-thymidine nucleoside and 5-propyne urindine nucleoside. In certain embodiments, each A comprises an HNA. In certain embodiments, each A comprises an F-HNA.

In certain embodiments, each W comprises a modified sugar moiety. In certain embodiments, each W comprises a 2′-substituted sugar moiety. In certain embodiments, each W comprises a 2′-substituted sugar moiety selected from among F, (ara)-F, OCH₃ and O(CH₂)₂—OCH₃. In certain embodiments, each W comprises a 5′-substituted sugar moiety. In certain embodiments, each W comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, each W comprises a bicyclic sugar moiety. In certain embodiments, each W comprises a bicyclic sugar moiety selected from among cEt, cMOE, LNA, α-L-LNA, ENA and 2′-thio LNA. In certain embodiments, each W comprises a sugar surrogate. In certain embodiments, each W comprises a sugar surrogate selected from among HNA and F-HNA.

In certain embodiments, at least one of A or B comprises a bicyclic sugar moiety, and the other comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-substituted sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-MOE sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-F sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside and the other of A or B comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-substituted sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-substituted sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-MOE sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-MOE sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-F sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-F sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-F sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-F sugar moiety.

In certain embodiments, A comprises a bicyclic sugar moiety, and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is an LNA nucleoside and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is a cEt nucleoside and B comprises a 2′-(ara)-F sugar moiety. In certain embodiments, A is an α-L-LNA nucleoside and B comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-MOE sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-MOE sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-F sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-F sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-F sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-F sugar moiety.

In certain embodiments, B comprises a bicyclic sugar moiety, and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is an LNA nucleoside and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is a cEt nucleoside and A comprises a 2′-(ara)-F sugar moiety. In certain embodiments, B is an α-L-LNA nucleoside and A comprises a 2′-(ara)-F sugar moiety.

In certain embodiments, at least one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-substituted sugar moiety and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and C comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a modified nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-substituted sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 2-thio-thymidine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises 2-thio-thymidine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and C comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and C comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and C comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5-propyne uridine nucleobase.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a sugar HNA surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a F-HNA sugar surrogate.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-MOE sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, one of A or B comprises a bicyclic sugar moiety, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is a cEt nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety. In certain embodiments, one of A or B is an α-L-LNA nucleoside, another of A or B comprises a 2′-(ara)-F sugar moiety, and W comprises a 5′-(R)-Me DNA sugar moiety.

In certain embodiments, at least two of A, B or W comprises a 2′-substituted sugar moiety, and the other comprises a bicyclic sugar moiety. In certain embodiments, at least two of A, B or W comprises a bicyclic sugar moiety, and the other comprises a 2′-substituted sugar moiety.

d. Certain Overall Lengths

In certain embodiments, the present invention provides oligomeric compounds including oligonucleotides of any of a variety of ranges of lengths. In certain embodiments, the invention provides oligomeric compounds or oligonucleotides consisting of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number of nucleosides in the range. In certain such embodiments, X and Y are each independently selected from 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50; provided that X<Y. For example, in certain embodiments, the invention provides oligomeric compounds which comprise oligonucleotides consisting of 8 to 9, 8 to 10, 8 to 11, 8 to 12, 8 to 13, 8 to 14, 8 to 15, 8 to 16, 8 to 17, 8 to 18, 8 to 19, 8 to 20, 8 to 21, 8 to 22, 8 to 23, 8 to 24, 8 to 25, 8 to 26, 8 to 27, 8 to 28, 8 to 29, 8 to 30, 9 to 10, 9 to 11, 9 to 12, 9 to 13, 9 to 14, 9 to 15, 9 to 16, 9 to 17, 9 to 18, 9 to 19, 9 to 20, 9 to 21, 9 to 22, 9 to 23, 9 to 24, 9 to 25, 9 to 26, 9 to 27, 9 to 28, 9 to 29, 9 to 30, 10 to 11, 10 to 12, 10 to 13, 10 to 14, 10 to 15, 10 to 16, 10 to 17, 10 to 18, 10 to 19, 10 to 20, 10 to 21, 10 to 22, 10 to 23, 10 to 24, 10 to 25, 10 to 26, 10 to 27, 10 to 28, 10 to 29, 10 to 30, 11 to 12, 11 to 13, 11 to 14, 11 to 15, 11 to 16, 11 to 17, 11 to 18, 11 to 19, 11 to 20, 11 to 21, 11 to 22, 11 to 23, 11 to 24, 11 to 25, 11 to 26, 11 to 27, 11 to 28, 11 to 29, 11 to 30, 12 to 13, 12 to 14, 12 to 15, 12 to 16, 12 to 17, 12 to 18, 12 to 19, 12 to 20, 12 to 21, 12 to 22, 12 to 23, 12 to 24, 12 to 25, 12 to 26, 12 to 27, 12 to 28, 12 to 29, 12 to 30, 13 to 14, 13 to 15, 13 to 16, 13 to 17, 13 to 18, 13 to 19, 13 to 20, 13 to 21, 13 to 22, 13 to 23, 13 to 24, 13 to 25, 13 to 26, 13 to 27, 13 to 28, 13 to 29, 13 to 30, 14 to 15, 14 to 16, 14 to 17, 14 to 18, 14 to 19, 14 to 20, 14 to 21, 14 to 22, 14 to 23, 14 to 24, 14 to 25, 14 to 26, 14 to 27, 14 to 28, 14 to 29, 14 to 30, 15 to 16, 15 to 17, 15 to 18, 15 to 19, 15 to 20, 15 to 21, 15 to 22, 15 to 23, 15 to 24, 15 to 25, 15 to 26, 15 to 27, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16 to 18, 16 to 19, 16 to 20, 16 to 21, 16 to 22, 16 to 23, 16 to 24, 16 to 25, 16 to 26, 16 to 27, 16 to 28, 16 to 29, 16 to 30, 17 to 18, 17 to 19, 17 to 20, 17 to 21, 17 to 22, 17 to 23, 17 to 24, 17 to 25, 17 to 26, 17 to 27, 17 to 28, 17 to 29, 17 to 30, 18 to 19, 18 to 20, 18 to 21, 18 to 22, 18 to 23, 18 to 24, 18 to 25, 18 to 26, 18 to 27, 18 to 28, 18 to 29, 18 to 30, 19 to 20, 19 to 21, 19 to 22, 19 to 23, 19 to 24, 19 to 25, 19 to 26, 19 to 29, 19 to 28, 19 to 29, 19 to 30, 20 to 21, 20 to 22, 20 to 23, 20 to 24, 20 to 25, 20 to 26, 20 to 27, 20 to 28, 20 to 29, 20 to 30, 21 to 22, 21 to 23, 21 to 24, 21 to 25, 21 to 26, 21 to 27, 21 to 28, 21 to 29, 21 to 30, 22 to 23, 22 to 24, 22 to 25, 22 to 26, 22 to 27, 22 to 28, 22 to 29, 22 to 30, 23 to 24, 23 to 25, 23 to 26, 23 to 27, 23 to 28, 23 to 29, 23 to 30, 24 to 25, 24 to 26, 24 to 27, 24 to 28, 24 to 29, 24 to 30, 25 to 26, 25 to 27, 25 to 28, 25 to 29, 25 to 30, 26 to 27, 26 to 28, 26 to 29, 26 to 30, 27 to 28, 27 to 29, 27 to 30, 28 to 29, 28 to 30, or 29 to 30 linked nucleosides. In embodiments where the number of nucleosides of an oligomeric compound or oligonucleotide is limited, whether to a range or to a specific number, the oligomeric compound or oligonucleotide may, nonetheless further comprise additional other substituents. For example, an oligonucleotide comprising 8-30 nucleosides excludes oligonucleotides having 31 nucleosides, but, unless otherwise indicated, such an oligonucleotide may further comprise, for example one or more conjugates, terminal groups, or other substituents. In certain embodiments, a gapmer oligonucleotide has any of the above lengths.

Further, where an oligonucleotide is described by an overall length range and by regions having specified lengths, and where the sum of specified lengths of the regions is less than the upper limit of the overall length range, the oligonucleotide may have additional nucleosides, beyond those of the specified regions, provided that the total number of nucleosides does not exceed the upper limit of the overall length range.

e. Certain Oligonucleotides

In certain embodiments, oligonucleotides of the present invention are characterized by their modification motif and overall length. In certain embodiments, such parameters are each independent of one another. Thus, unless otherwise indicated, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. For example, the internucleoside linkages within the wing regions of a sugar-gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region. Likewise, such sugar-gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications. One of skill in the art will appreciate that such motifs may be combined to create a variety of oligonucleotides. Herein if a description of an oligonucleotide or oligomeric compound is silent with respect to one or more parameter, such parameter is not limited. Thus, an oligomeric compound described only as having a gapmer sugar motif without further description may have any length, internucleoside linkage motif, and nucleobase modification motif. Unless otherwise indicated, all chemical modifications are independent of nucleobase sequence.

f. Certain Conjugate Groups

In certain embodiments, oligomeric compounds are modified by attachment of one or more conjugate groups. In general, conjugate groups modify one or more properties of the attached oligomeric compound including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, cellular distribution, cellular uptake, charge and clearance. Conjugate groups are routinely used in the chemical arts and are linked directly or via an optional conjugate linking moiety or conjugate linking group to a parent compound such as an oligomeric compound, such as an oligonucleotide. Conjugate groups includes without limitation, intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes. Certain conjugate groups have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937).

In certain embodiments, a conjugate group comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.

In certain embodiments, conjugate groups are directly attached to oligonucleotides in oligomeric compounds. In certain embodiments, conjugate groups are attached to oligonucleotides by a conjugate linking group. In certain such embodiments, conjugate linking groups, including, but not limited to, bifunctional linking moieties such as those known in the art are amenable to the compounds provided herein.

Conjugate linking groups are useful for attachment of conjugate groups, such as chemical stabilizing groups, functional groups, reporter groups and other groups to selective sites in a parent compound such as for example an oligomeric compound. In general a bifunctional linking moiety comprises a hydrocarbyl moiety having two functional groups. One of the functional groups is selected to bind to a parent molecule or compound of interest and the other is selected to bind essentially any selected group such as chemical functional group or a conjugate group. In some embodiments, the conjugate linker comprises a chain structure or an oligomer of repeating units such as ethylene glycol or amino acid units. Examples of functional groups that are routinely used in a bifunctional linking moiety include, but are not limited to, electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups. In some embodiments, bifunctional linking moieties include amino, hydroxyl, carboxylic acid, thiol, unsaturations (e.g., double or triple bonds), and the like.

Some nonlimiting examples of conjugate linking moieties include pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA). Other linking groups include, but are not limited to, substituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl or substituted or unsubstituted C₂-C₁₀ alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.

Conjugate groups may be attached to either or both ends of an oligonucleotide (terminal conjugate groups) and/or at any internal position.

In certain embodiments, conjugate groups are at the 3′-end of an oligonucleotide of an oligomeric compound. In certain embodiments, conjugate groups are near the 3′-end. In certain embodiments, conjugates are attached at the 3′end of an oligomeric compound, but before one or more terminal group nucleosides. In certain embodiments, conjugate groups are placed within a terminal group.

In certain embodiments, the present invention provides oligomeric compounds. In certain embodiments, oligomeric compounds comprise an oligonucleotide. In certain embodiments, an oligomeric compound comprises an oligonucleotide and one or more conjugate and/or terminal groups. Such conjugate and/or terminal groups may be added to oligonucleotides having any of the motifs discussed above. Thus, for example, an oligomeric compound comprising an oligonucleotide having region of alternating nucleosides may comprise a terminal group.

C. Antisense Compounds

In certain embodiments, oligomeric compounds provided herein are antisense compounds. Such antisense compounds are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, antisense compounds specifically hybridize to one or more target nucleic acid. In certain embodiments, a specifically hybridizing antisense compound has a nucleobase sequence comprising a region having sufficient complementarity to a target nucleic acid to allow hybridization and result in antisense activity and insufficient complementarity to any non-target so as to avoid non-specific hybridization to any non-target nucleic acid sequences under conditions in which specific hybridization is desired (e.g., under physiological conditions for in vivo or therapeutic uses, and under conditions in which assays are performed in the case of in vitro assays).

In certain embodiments, the present invention provides antisense compounds comprising oligonucleotides that are fully complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are 95% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 90% complementary to the target nucleic acid.

In certain embodiments, such oligonucleotides are 85% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 80% complementary to the target nucleic acid. In certain embodiments, an antisense compound comprises a region that is fully complementary to a target nucleic acid and is at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain such embodiments, the region of full complementarity is from 6 to 14 nucleobases in length.

a. Certain Antisense Activities and Mechanisms

In certain antisense activities, hybridization of an antisense compound results in recruitment of a protein that cleaves of the target nucleic acid. For example, certain antisense compounds result in RNase H mediated cleavage of target nucleic acid. RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. The “DNA” in such an RNA:DNA duplex, need not be unmodified DNA. In certain embodiments, the invention provides antisense compounds that are sufficiently “DNA-like” to elicit RNase H activity. Such DNA-like antisense compounds include, but are not limited to gapmers having unmodified deoxyfuronose sugar moieties in the nucleosides of the gap and modified sugar moieties in the nucleosides of the wings.

Antisense activities may be observed directly or indirectly. In certain embodiments, observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid; a change in the ratio of splice variants of a nucleic acid or protein; and/or a phenotypic change in a cell or animal.

In certain embodiments, compounds comprising oligonucleotides having a gapmer nucleoside motif described herein have desirable properties compared to non-gapmer oligonucleotides or to gapmers having other motifs. In certain circumstances, it is desirable to identify motifs resulting in a favorable combination of potent antisense activity and relatively low toxicity. In certain embodiments, compounds of the present invention have a favorable therapeutic index (measure of activity divided by measure of toxicity).

b. Certain Selective Antisense Compounds

In certain embodiments, antisense compounds provided are selective for a target relative to a non-target nucleic acid. In certain embodiments, the nucleobase sequences of the target and non-target nucleic acids differ by no more than 4 differentiating nucleobases in the targeted region. In certain embodiments, the nucleobase sequences of the target and non-target nucleic acids differ by no more than 3 differentiating nucleobases in the targeted region. In certain embodiments, the nucleobase sequences of the target and non-target nucleic acids differ by no more than 2 differentiating nucleobases in the targeted region. In certain embodiments, the nucleobase sequences of the target and non-target nucleic acids differ by a single differentiating nucleobase in the targeted region. In certain embodiments, the target and non-target nucleic acids are transcripts from different genes. In certain embodiments, the target and non-target nucleic acids are different alleles for the same gene. In certain embodiments, the introduction of a mismatch between an antisense compound and a non-target nucleic acid may alter the RNase H cleavage site of a target nucleic acid compared to a non-target nucleic acid. In certain embodiments, the target and non-target nucleic acids are not functionally related to one another (e.g., are transcripts from different genes). In certain embodiments, the target and not-target nucleic acids are allelic variants of one another. In certain embodiments, the allelic variant contains a single nucleotide polymorphism (SNP). In certain embodiments, a SNP is associated with a mutant allele. In certain embodiments, a mutant SNP is associated with a disease. In certain embodiments a mutant SNP is associated with a disease, but is not causative of the disease. In certain embodiments, mRNA and protein expression of a mutant allele is associated with disease.

Selectivity of antisense compounds is achieved, principally, by nucleobase complementarity. For example, if an antisense compound has no mismatches for a target nucleic acid and one or more mismatches for a non-target nucleic acid, some amount of selectivity for the target nucleic acid will result. In certain embodiments, provided herein are antisense compounds with enhanced selectivity (i.e. the ratio of activity for the target to the activity for non-target is greater). For example, in certain embodiments, a selective nucleoside comprises a particular feature or combination of features (e.g., chemical modification, motif, placement of selective nucleoside, and/or self-complementary region) that increases selectivity of an antisense compound compared to an antisense compound not having that feature or combination of features.

In certain embodiments, such feature or combination of features increases antisense activity for the target. In certain embodiments, such feature or combination of features decreases activity for the target, but decreases activity for the non-target by a greater amount, thus resulting in an increase in selectivity.

Without being limited by mechanism, enhanced selectivity may result from a larger difference in the affinity of an antisense compound for its target compared to its affinity for the non-target and/or a larger difference in RNase H activity for the resulting duplexes. For example, in certain embodiments, a selective antisense compound comprises a modified nucleoside at that same position as a differentiating nucleobase (i.e., the selective nucleoside is modified). That modification may increase the difference in binding affinity of the antisense compound for the target relative to the non-target. In addition or in the alternative, the chemical modification may increase the difference in RNAse H activity for the duplex formed by the antisense compound and its target compared to the RNase activity for the duplex formed by the antisense compound and the non-target. For example, the modification may exaggerate a structure that is less compatible for RNase H to bind, cleave and/or release the non-target.

In certain embodiments, an antisense compound binds its intended target to form a target duplex. In certain embodiments, RNase H cleaves the target nucleic acid of the target duplex. In certain such embodiments, there is a primary cleavage site between two particular nucleosides of the target nucleic acid (the primary target cleavage site), which accounts for the largest amount of cleavage of the target nucleic acid. In certain nembodiments, there are one or more secondary target cleavage sites. In certain embodiments, the same antisence compound hybridizes to a non-target to form a non-target duplex. In certain such embodiments, the non-target differs from the target by a single nucleobase within the target region, and so the antisense compound hybridizes with a single mismatch. Because of the mismatch, in certain embodiments, RNase H cleavage of the non-target may be reduced compared to cleavage of the target, but still occurs. In certain embodiments, though, the primary site of that cleavage of the non-target nucleic acid (primary non-target cleavage site) is different from that of the target. That is; the primary site is shifted due to the mismatch. In such a circumstance, one may use a modification placed in the antisense compound to disrupt RNase H cleavage at the primary non-target cleavage site. Such modification will result in reduced cleavage of the non-target, but will result little or no decrease in cleavage of the target. In certain embodiments, the modification is a modified sugar, nucleobase and/or linkage.

In certain embodiments, the primary non-target cleavage site is towards the 5′-end of the antisense compound, and the 5′-end of an antisense compound may be modified to prevent RNaseH cleavage. In this manner, it is thought that one having skill in the art may modify the 5′-end of an antisense compound, or modify the nucleosides in the gap region of the 5′-end of the antisense compound, or modify the the 3′-most 5′-region nucleosides of the antisense compound to selectively inhibit RNaseH cleavage of the non-target nucleic acid duplex while retaining RNase H cleavage of the target nucleic acid duplex. In certain embodiments, 1-3 of the 3′-most 5′-region nucleosides of the antisense compound comprises a bicyclic sugar moiety.

For example, in certain embodiments the target nucleic acid may have an allelic variant, e.g. a non-target nucleic acid, containing a single nucleotide polymorphism. An antisense compound may be designed having a single nucleobase mismatch from the non-target nucleic acid, but which has full complementarity to the target nucleic acid. The mismatch between the antisense compound and the non-target nucleic acid may destabilize the antisense compound non-target nucleic acid duplex, and consequently the cleavage site of RNaseH may shift upstream towards the 5′-end of the antisense compound. Modification of the 5′-end of the antisense compound or the gap region near the 5′-end of the antisense compound, or one or more of the 3′-most nucleosides of the 5′-wing region, will then prevent RNaseH cleavage of the non-target nucleic acid. Since the target nucleic acid is fully complementary to the antisense compound, the antisense compound and the target nucleic acid will form a more stabilized antisense compound-target nucleic acid duplex and the cleavage site of RnaseH will be more downstream, towards the 3′ end of the antisense compound. Accordingly, modifications at the 5′-end of the antisense compound will prevent RNaseH cleavage of the non-target nucleic acid, but will not substantially effect RNaseH cleavage of the target nucleic acid, and selectivity between a target nucleic acid and its allelic variant may be achieved. In certain embodiments, one or more of the 3′-most nucleosides of the 5′-wing region comprises a bicyclic sugar moiety. In certain embodiments, one or more of the 3′-most nucleosides of the 5′-wing region comprises a bicyclic sugar moiety selected from cEt and LNA. In certain embodiments, one or more of the 3′-most nucleosides of the 5′-wing region comprises cEt. In certain embodiments, one or more of the 3′-most nucleosides of the 5′-wing region comprises LNA.

In certain embodiments, the introduction of a mismatch between an antisense compound and a target nucleic acid may alter the RNase H cleavage site of a target nucleic acid compared to a non-target nucleic acid by shifting the RNaseH cleavage site downstream from the mismatch site and towards the 3′-end of the antisense compound. In certain embodiments where the cleavage site of a target nucleic acid compared to a non-target nucleic acid has shifted downstream towards the 3′-end of the antisense compound, the 3′-end of an antisense compound may be modified to prevent RNaseH cleavage. In this manner, it is thought that one having skill in the art may modify the 3′-end of an antisense compound, or modify the nucleosides in the gap region near the 3′-end of antisense compound, to selectively inhibit RNaseH cleavage of the non-target nucleic acid while retaining RNase H cleavage of the target nucleic acid.

For example, in certain embodiments the target nucleic acid may have an allelic variant, e.g. a non-target nucleic acid, containing a single nucleotide polymorphism. An antisense compound may be designed having a single nucleobase mismatch from the non-target nucleic acid, but which has full complementarity to target nucleic acid. The mismatch between the antisense compound and the non-target nucleic acid may destabilize the antisense compound-non-target nucleic acid duplex, and consequently the cleavage site of RNaseH may shift downstream towards the 3′-end of the antisense compound. Modification of the 3′-end of the antisense compound, or one or more of the the 5′-most nucleosides of the 3′-wing region, or the gap region of the antisense compound near the 3′-end will then prevent RNaseH cleavage of the non-target nucleic acid. Since the target nucleic acid is fully complementary to the antisense compound, the antisense compound and the target nucleic acid will form a more stabilized antisense compound-target nucleic acid duplex and the cleavage site of RnaseH will be more upstream, towards the 5′ end of the antisense compound. Accordingly, modifications at the 3′-end of the antisense compound will prevent RNaseH cleavage of the non-target nucleic acid, but will not substantially effect RNaseH cleavage of the target nucleic acid, and selectivity between a target nucleic acid and its allelic variant may be achieved. In certain embodiments, one or more of the 5′-most nucleosides of the 3′-wing region comprises a bicyclic sugar moiety. In certain embodiments, one or more of the 5′-most nucleosides of the 3′-wing region comprises a bicyclic sugar moiety selected from cEt and LNA. In certain embodiments, one or more of the 5′-most nucleosides of the 3′-wing region comprises cEt. In certain embodiments, one or more of the 5′-most nucleosides of the 3′-wing region comprises LNA.

In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of one or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of two or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of one bicyclic nucleoside at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of two bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of three bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of four bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of five bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside are selected from among cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside comprise cEt. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside comprise LNA.

In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of one or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of two or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of one bicyclic nucleoside at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of two bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of three bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of four bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or longer, may be improved by the addition of four bicyclic nucleosides at the 3′-most 5′-wing nucleoside and the addition of one or more bicyclic nucleosides at the 5′-most 3′-wing nucleoside.

In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of one or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of two or more bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of one bicyclic nucleoside at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of two bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of three bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of four bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments, the selectivity of antisense compounds having certain gaps, e.g. gaps of 7 nucleosides or shorter, may be improved by the addition of five bicyclic nucleosides at the 3′-most 5′-wing nucleoside. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside are selected from among cEt, cMOE, LNA, α-LNA, ENA and 2′-thio LNA. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside comprise cEt. In certain embodiments discussed above, the bicyclic nucleosides at the 3′-most 5′-wing nucleoside comprise LNA.

Antisense compounds having certain specified motifs have enhanced selectivity, including, but not limited to motifs described above. In certain embodiments, enhanced selectivity is achieved by oligonucleotides comprising any one or more of:

a modification motif comprising a long 5′-wing (longer than 5, 6, or 7 nucleosides);

a modification motif comprising a long 3′-wing (longer than 5, 6, or 7 nucleosides);

a modification motif comprising a short gap region (shorter than 8, 7, or 6 nucleosides); and

a modification motif comprising an interrupted gap region (having no uninterrupted stretch of unmodified 2′-deoxynucleosides longer than 7, 6 or 5).

i. Certain Selective Nucleobase Sequence Elements

In certain embodiments, selective antisense compounds comprise nucleobase sequence elements. Such nucleobase sequence elements are independent of modification motifs. Accordingly, oligonucleotides having any of the motifs (modification motifs, nucleoside motifs, sugar motifs, nucleobase modification motifs, and/or linkage motifs) may also comprise one or more of the following nucleobase sequence elements.

ii. Alignment of Differentiating Nucleobase/Target-Selective Nucleoside

In certain embodiments, a target region and a region of a non-target nucleic acid differ by 1-4 differentiating nucleobase. In such embodiments, selective antisense compounds have a nucleobase sequence that aligns with the non-target nucleic acid with, 1-4 mismatches. A nucleoside of the antisense compound that corresponds to a differentiating nucleobase of the target nucleic acid is referred to herein as a target-selective nucleoside. In certain embodiments, selective antisense compounds having a gapmer motif align with a non-target nucleic acid, such that a target-selective nucleoside is positioned in the gap. In certain embodiments, a target-selective nucleoside is the 1^(st) nucleoside of the gap from the 5′ end. In certain embodiments, a target-selective nucleoside is the 2^(nd) nucleoside of the gap from the 5′ end. In certain embodiments, a target-selective nucleoside is the 3^(rd) nucleoside of the gap from the 5′-end. In certain embodiments, a target-selective nucleoside is the 4^(th) nucleoside of the gap from the 5′-end. In certain embodiments, a target-selective nucleoside is the 5^(th) nucleoside of the gap from the 5′-end. In certain embodiments, a target-selective nucleoside is the 6^(rd) nucleoside of the gap from the 5′-end. In certain embodiments, a target-selective nucleoside is the 8^(th) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 7^(th) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 6^(th) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 5^(th) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 4^(th) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 3^(rd) nucleoside of the gap from the 3′-end. In certain embodiments, a target-selective nucleoside is the 2^(nd) nucleoside of the gap from the 3′-end.

In certain embodiments, a target-selective nucleoside comprises a modified nucleoside. In certain embodiments, a target-selective nucleoside comprises a modified sugar. In certain embodiments, a target-selective nucleoside comprises a sugar surrogate. In certain embodiments, a target-selective nucleoside comprises a sugar surrogate selected from among HNA and F-HNA. In certain embodiments, a target-selective nucleoside comprises a 2′-substituted sugar moiety. In certain embodiments, a target-selective nucleoside comprises a 2′-substituted sugar moiety selected from among MOE, F and (ara)-F. In certain embodiments, a target-selective nucleoside comprises a 5′-substituted sugar moiety. In certain embodiments, a target-selective nucleoside comprises a 5′-substituted sugar moiety selected from 5′-(R)-Me DNA. In certain embodiments, a target-selective nucleoside comprises a bicyclic sugar moiety. In certain embodiments, a target-selective nucleoside comprises a bicyclic sugar moiety selected from among cEt, and α-L-LNA. In certain embodiments, a target-selective nucleoside comprises a modified nucleobase. In certain embodiments, a target-selective nucleoside comprises a modified nucleobase selected from among 2-thio-thymidine and 5-propyne uridine.

iii. Mismatches to the Target Nucleic Acid

In certain embodiments, selective antisense compounds comprise one or more mismatched nucleobases relative to the target nucleic acid. In certain such embodiments, antisense activity against the target is reduced by such mismatch, but activity against the non-target is reduced by a greater amount. Thus, in certain embodiments selectivity is improved. Any nucleobase other than the differentiating nucleobase is suitable for a mismatch. In certain embodiments, however, the mismatch is specifically positioned within the gap of an oligonucleotide having a gapmer motif. In certain embodiments, a mismatch relative to the target nucleic acid is at positions 1, 2, 3, 4, 5, 6, 7, or 8 from the 5′-end of the gap region. In certain embodiments, a mismatch relative to the target nucleic acid is at positions 9, 8, 7, 6, 5, 4, 3, 2, 1 of the antisense compounds from the 3′-end of the gap region. In certain embodiments, a mismatch relative to the target nucleic acid is at positions 1, 2, 3, or 4 of the antisense compounds from the 5′-end of the wing region. In certain embodiments, a mismatch relative to the target nucleic acid is at positions 4, 3, 2, or 1 of the antisense compounds from the 3′-end of the wing region.

iv. Self Complementary Regions

In certain embodiments, selective antisense compounds comprise a region that is not complementary to the target. In certain embodiments, such region is complementary to another region of the antisense compound. Such regions are referred to herein as self-complementary regions. For example, in certain embodiments, an antisense compound has a first region at one end that is complementary to a second region at the other end. In certain embodiments, one of the first and second regions is complementary to the target nucleic acid. Unless the target nucleic acid also includes a self-complementary region, the other of the first and second region of the antisense compound will not be complementary to the target nucleic acid. For illustrative purposes, certain antisense compounds have the following nucleobase motif:

ABCXXXXXXXXXC′B′A′; ABCXXXXXXX(X/C′)(X/B′)(X/A′); (X/A)(X/B)(X/C)XXXXXXXXXC′B′A′ where each of A, B, and C are any nucleobase; A′, B′, and C′ are the complementary bases to A, B, and C, respectively; each X is a nucleobase complementary to the target nucleic acid; and two letters in parentheses (e.g., (X/C′)) indicates that the nucleobase is complementary to the target nucleic acid and to the designated nucleoside within the antisense oligonucleotide.

Without being bound to any mechanism, in certain embodiments, such antisense compounds are expected to form self-structure, which is disrupted upon contact with a target nucleic acid. Contact with a non-target nucleic acid is expected to disrupt the self-structure to a lesser degree, thus increasing selectivity compared to the same antisense compound lacking the self-complementary regions.

v. Combinations of Features

Though it is clear to one of skill in the art, the above motifs and other elements for increasing selectivity may be used alone or in combination. For example, a single antisense compound may include any one, two, three, or more of: self-complementary regions, a mismatch relative to the target nucleic acid, a short nucleoside gap, an interrupted gap, and specific placement of the selective nucleoside.

D. Certain Target Nucleic Acids

In certain embodiments, antisense compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid. In certain embodiments, the target nucleic acid is an endogenous RNA molecule. In certain embodiments, the target nucleic acid is a non-coding RNA. In certain such embodiments, the target non-coding RNA is selected from: a long-non-coding RNA, a short non-coding RNA, an intronic RNA molecule, a snoRNA, a scaRNA, a microRNA (including pre-microRNA and mature microRNA), a ribosomal RNA, and promoter directed RNA. In certain embodiments, the target nucleic acid encodes a protein. In certain such embodiments, the target nucleic acid is selected from: an mRNA and a pre-mRNA, including intronic, exonic and untranslated regions. In certain embodiments, oligomeric compounds are at least partially complementary to more than one target nucleic acid. For example, antisense compounds of the present invention may mimic microRNAs, which typically bind to multiple targets.

In certain embodiments, the target nucleic acid is a nucleic acid other than a mature mRNA. In certain embodiments, the target nucleic acid is a nucleic acid other than a mature mRNA or a microRNA. In certain embodiments, the target nucleic acid is a non-coding RNA other than a microRNA. In certain embodiments, the target nucleic acid is a non-coding RNA other than a microRNA or an intronic region of a pre-mRNA. In certain embodiments, the target nucleic acid is a long non-coding RNA. In certain embodiments, the target RNA is an mRNA. In certain embodiments, the target nucleic acid is a pre-mRNA.

In certain such embodiments, the target region is entirely within an intron. In certain embodiments, the target region spans an intron/exon junction. In certain embodiments, the target region is at least 50% within an intron. In certain embodiments, the target nucleic acid is selected from among non-coding RNA, including exonic regions of pre-mRNA. In certain embodiments, the target nucleic acid is a ribosomal RNA (rRNA). In certain embodiments, the target nucleic acid is a non-coding RNA associated with splicing of other pre-mRNAs. In certain embodiments, the target nucleic acid is a nuclear-retained non-coding RNA.

In certain embodiments, antisense compounds described herein are complementary to a target nucleic acid comprising a single-nucleotide polymorphism. In certain such embodiments, the antisense compound is capable of modulating expression of one allele of the single-nucleotide polymorphism-containing-target nucleic acid to a greater or lesser extent than it modulates another allele. In certain embodiments an antisense compound hybridizes to a single-nucleotide polymorphism-containing-target nucleic acid at the single-nucleotide polymorphism site. In certain embodiments, the target nucleic acid is a Huntingtin gene transcript.

In certain embodiments, the target nucleic acid is a single-nucleotide polymorphism-containing-target nucleic acid of a Huntingtin gene transcript. In certain embodiments, the target nucleic acid is not a Huntingtin gene transcript. In certain embodiments, the target nucleic acid is a single-nucleotide polymorphism-containing-target nucleic acid of a gene transcript other than Huntingtin. In certain embodiments, the target nucleic acid is any nucleic acid other than a Huntingtin gene transcript.

a. Single-Nucleotide Polymorphism

In certain embodiments, the invention provides selective antisense compounds that have greater activity for a target nucleic acid than for a homologous or partially homologous non-target nucleic acid. In certain such embodiments, the target and non-target nucleic acids are not functionally related to one another (e.g., are transcripts from different genes). In certain embodiments, the target and not-targe nucleic acids are allelic variants of one another. Certain embodiments of the present invention provide methods, compounds, and compositions for selectively inhibiting mRNA and protein expression of an allelic variant of a particular gene or DNA sequence. In certain embodiments, the allelic variant contains a single nucleotide polymorphism (SNP). In certain embodiments, a SNP is associated with a mutant allele. In certain embodiments, a mutant SNP is associated with a disease. In certain embodiments a mutant SNP is associated with a disease, but is not causative of the disease. In certain embodiments, mRNA and protein expression of a mutant allele is associated with disease.

In certain embodiments, the expressed gene product of a mutant allele results in aggregation of the mutant proteins causing disease. In certain embodiments, the expressed gene product of a mutant allele results in gain of function causing disease. In certain embodiments, genes with an autosomal dominant mutation resulting in a toxic gain of function of the protein are the APP gene encoding amyloid precursor protein involved in Alzheimer's disease (Gene, 371: 68, 2006); the PrP gene encoding prion protein involved in Creutzfeldt-Jakob disease and in fatal familial insomnia (Nat. Med. 1997, 3: 1009); GFAP gene encoding glial fibrillary acidic protein involved in Alexander disease (J. Neurosci. 2006, 26:111623); alpha-synuclein gene encoding alpha-synuclein protein involved in Parkinson's disease (J. Clin. Invest. 2003, 111: 145); SOD-1 gene encoding the SOD-1 protein involved in amyotrophic lateral sclerosis (Science 1998, 281: 1851); atrophin-1 gene encoding atrophin-1 protein involved in dentato-rubral and pallido-luysian atrophy (DRPA) (Trends Mol. Med. 2001, 7: 479); SCA1 gene encoding ataxin-1 protein involved in spino-cerebellar ataxia-1 (SCA1) (Protein Sci. 2003, 12: 953); PLP gene encoding proteolipid protein involved in Pelizaeus-Merzbacher disease (NeuroMol Med. 2007, 4: 73); DYT1 gene encoding torsinA protein involved in Torsion dystonia (Brain Res. 2000, 877: 379); and alpha-B crystalline gene encoding alpha-B crystalline protein involved in protein aggregation diseases, including cardiomyopathy (Cell 2007, 130: 427); alphal-antitrypsin gene encoding alphal-antitrypsin protein involved in chronic obstructive pulmonary disease (COPD), liver disease and hepatocellular carcinoma (New Engl J Med. 2002, 346: 45); Ltk gene encoding leukocyte tyrosine kinase protein involved in systemic lupus erythematosus (Hum. Mol. Gen. 2004, 13: 171); PCSK9 gene encoding PCSK9 protein involved in hypercholesterolemia (Hum Mutat. 2009, 30: 520); prolactin receptor gene encoding prolactin receptor protein involved in breast tumors (Proc. Natl. Assoc. Sci. 2008, 105: 4533); CCL5 gene encoding the chemokine CCL5 involved in COPD and asthma (Eur. Respir. J. 2008, 32: 327); PTPN22 gene encoding PTPN22 protein involved in Type 1 diabetes, Rheumatoid arthritis, Graves disease, and SLE (Proc. Natl. Assoc. Sci. 2007, 104: 19767); androgen receptor gene encoding the androgen receptor protein involved in spinal and bulbar muscular atrophy or Kennedy's disease (J Steroid Biochem. Mol. Biol. 2008, 108: 245); CHMP4B gene encoding chromatin modifying protein-4B involved in progressive childhood posterior subcapsular cataracts (Am. J. Hum. Genet 2007, 81: 596); FXR/NR1H4 gene encoding Farnesoid X receptor protein involved in cholesterol gallstone disease, arthrosclerosis and diabetes (Mol. Endocrinol. 2007, 21: 1769); ABCA1 gene encoding ABCA1 protein involved in cardiovascular disease (Transl. Res. 2007, 149: 205); CaSR gene encoding the calcium sensing receptor protein involved in primary hypercalciuria (Kidney Int. 2007, 71: 1155); alpha-globin gene encoding alpha-globin protein involved in alpha-thallasemia (Science 2006, 312: 1215); httlpr gene encoding HTTLPR protein involved in obsessive compulsive disorder (Am. J. Hum. Genet. 2006, 78: 815); AVP gene encoding arginine vasopressin protein in stress-related disorders such as anxiety disorders and comorbid depression (CNS Neurol. Disord. Drug Targets 2006, 5: 167); GNAS gene encoding G proteins involved in congenital visual defects, hypertension, metabolic syndrome (Trends Pharmacol. Sci. 2006, 27: 260); APAF1 gene encoding APAF1 protein involved in a predisposition to major depression (Mol. Psychiatry 2006, 11: 76); TGF-beta1 gene encoding TGF-beta1 protein involved in breast cancer and prostate cancer (Cancer Epidemiol. Biomarkers Prev. 2004, 13: 759); AChR gene encoding acetylcholine receptor involved in congential myasthenic syndrome (Neurology 2004, 62: 1090); P2Y12 gene encoding adenosine diphosphate (ADP) receptor protein involved in risk of peripheral arterial disease (Circulation 2003, 108: 2971); LQT1 gene encoding LQT1 protein involved in atrial fibrillation (Cardiology 2003, 100: 109); RET protooncogene encoding RET protein involved in sporadic pheochromocytoma (J. Clin. Endocrinol. Metab. 2003, 88: 4911); filamin A gene encoding filamin A protein involved in various congenital malformations (Nat. Genet. 2003, 33: 487); TARDBP gene encoding TDP-43 protein involved in amyotrophic lateral sclerosis (Hum. Mol. Gene.t 2010, 19: 671); SCA3 gene encoding ataxin-3 protein involved in Machado-Joseph disease (PLoS One 2008, 3: e3341); SCA7 gene encoding ataxin-7 protein involved in spino-cerebellar ataxia-7 (PLoS One 2009, 4: e7232); and HTT gene encoding huntingtin protein involved in Huntington's disease (Neurobiol Dis. 1996, 3:183); and the CA4 gene encoding carbonic anhydrase 4 protein, CRX gene encoding cone-rod homeobox transcription factor protein, FSCN2 gene encoding retinal fascin homolog 2 protein, IMPDH1 gene encoding inosine monophosphate dehydrogenase 1 protein, NR2E3 gene encoding nuclear receptor subfamily 2 group E3 protein, NRL gene encoding neural retina leucine zipper protein, PRPF3 (RP 18) gene encoding pre-mRNA splicing factor 3 protein, PRPF8 (RP13) gene encoding pre-mRNA splicing factor 8 protein, PRPF31 (RP11) gene encoding pre-mRNA splicing factor 31 protein, RDS gene encoding peripherin 2 protein, ROM1 gene encoding rod outer membrane protein 1 protein, RHO gene encoding rhodopsin protein, RP1 gene encoding RP1 protein, RPGR gene encoding retinitis pigmentosa GTPase regulator protein, all of which are involved in Autosomal Dominant Retinitis Pigmentosa disease (Adv Exp Med Biol. 2008, 613:203)

In certain embodiments, the mutant allele is associated with any disease from the group consisting of Alzheimer's disease, Creutzfeldt-Jakob disease, fatal familial insomnia, Alexander disease, Parkinson's disease, amyotrophic lateral sclerosis, dentato-rubral and pallido-luysian atrophy DRPA, spino-cerebellar ataxia, Torsion dystonia, cardiomyopathy, chronic obstructive pulmonary disease (COPD), liver disease, hepatocellular carcinoma, systemic lupus erythematosus, hypercholesterolemia, breast cancer, asthma, Type 1 diabetes, Rheumatoid arthritis, Graves disease, SLE, spinal and bulbar muscular atrophy, Kennedy's disease, progressive childhood posterior subcapsular cataracts, cholesterol gallstone disease, arthrosclerosis, cardiovascular disease, primary hypercalciuria, alpha-thallasemia, obsessive compulsive disorder, Anxiety, comorbid depression, congenital visual defects, hypertension, metabolic syndrome, prostate cancer, congential myasthenic syndrome, peripheral arterial disease, atrial fibrillation, sporadic pheochromocytoma, congenital malformations, Machado-Joseph disease, Huntington's disease, and Autosomal Dominant Retinitis Pigmentosa disease.

i. Certain Huntingtin Targets

In certain embodiments, an allelic variant of huntingtin is selectively reduced. Nucleotide sequences that encode huntingtin include, without limitation, the following: GENBANK Accession No. NT_006081.18, truncated from nucleotides 1566000 to 1768000 (replaced by GENBANK Accession No. NT_006051), incorporated herein as SEQ ID NO: 1, and NM_002111.6, incorporated herein as SEQ ID NO: 2.

Table 14 provides SNPs found in the GM04022, GM04281, GM02171, and GM02173B cell lines. Also provided are the allelic variants found at each SNP position, the genotype for each of the cell lines, and the percentage of HD patients having a particular allelic variant. For example, the two allelic variants for SNP rs6446723 are T and C. The GM04022 cell line is heterozygous TC, the GM02171 cell line is homozygous CC, the GM02173 cell line is heterozygous TC, and the GM04281 cell line is homozygous TT. Fifty percent of HD patients have a T at SNP position rs6446723.

TABLE 14 Allelic Variations for SNPs Associated with HD SNP Variation GM04022 GM02171 GM02173 GM04281 TargetPOP allele rs6446723 T/C TC CC TC TT 0.50 T rs3856973 A/G AG AA AG GG 0.50 G rs2285086 A/G AG GG AG AA 0.50 A rs363092 A/C AC AA AC CC 0.49 C rs916171 C/G GC GG GC CC 0.49 C rs6844859 T/C TC CC TC TT 0.49 T rs7691627 A/G AG AA AG GG 0.49 G rs4690073 A/G AG AA AG GG 0.49 G rs2024115 A/G AG GG AG AA 0.48 A rs11731237 T/C CC CC TC TT 0.43 T rs362296 A/C CC AC AC AC 0.42 C rs10015979 A/G AA AA AG GG 0.42 G rs7659144 C/G CG CG CG CC 0.41 C rs363096 T/C CC CC TC TT 0.40 T rs362273 A/G AA AG AG AA 0.39 A rs16843804 T/C CC TC TC CC 0.38 C rs362271 A/G GG AG AG GG 0.38 G rs362275 T/C CC TC TC CC 0.38 C rs3121419 T/C CC TC TC CC 0.38 C rs362272 A/G GG — AG GG 0.38 G rs3775061 A/G AA AG AG AA 0.38 A rs34315806 T/C CC TC TC CC 0.38 C rs363099 T/C CC TC TC CC 0.38 C rs2298967 T/C TT TC TC TT 0.38 T rs363088 A/T AA TA TA AA 0.38 A rs363064 T/C CC TC TC CC 0.35 C rs363102 A/G AG AA AA AA 0.23 G rs2798235 A/G AG GG GG GG 0.21 A rs363080 T/C TC CC CC CC 0.21 T rs363072 A/T TA TA AA AA 0.13 A rs363125 A/C AC AC CC CC 0.12 C rs362303 T/C TC TC CC CC 0.12 C rs362310 T/C TC TC CC CC 0.12 C rs10488840 A/G AG AG GG GG 0.12 G rs362325 T/C TC TC TT TT 0.11 T rs35892913 A/G GG GG GG GG 0.10 A rs363102 A/G AG AA AA AA 0.09 A rs363096 T/C CC CC TC TT 0.09 C rs11731237 T/C CC CC TC TT 0.09 C rs10015979 A/G AA AA AG GG 0.08 A rs363080 T/C TC CC CC CC 0.07 C rs2798235 A/G AG GG GG GG 0.07 G rs1936032 C/G GC CC CC CC 0.06 C rs2276881 A/G GG GG GG GG 0.06 G rs363070 A/G AA AA AA AA 0.06 A rs35892913 A/G GG GG GG GG 0.04 G rs12502045 T/C CC CC CC CC 0.04 C rs6446723 T/C TC CC TC TT 0.04 C rs7685686 A/G AG GG AG AA 0.04 G rs3733217 T/C CC CC CC CC 0.03 C rs6844859 T/C TC CC TC TT 0.03 C rs362331 T/C TC CC TC TT 0.03 C

E. Certain Indications

In certain embodiments, provided herein are methods of treating an animal or individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual or animal has Huntington's disease.

In certain embodiments, compounds targeted to huntingtin as described herein may be administered to reduce the severity of physiological symptoms of Huntington's disease. In certain embodiments, compounds targeted to huntingtin as described herein may be administered to reduce the rate of degeneration in an individual or an animal having Huntington's disease. In certain embodiments, compounds targeted to huntingtin as described herein may be administered regeneration function in an individual or an animal having Huntington's disease. In certain embodiments, symptoms of Huntingtin's disease may be reversed by treatment with a compound as described herein.

In certain embodiments, compounds targeted to huntingtin as described herein may be administered to ameliorate one or more symptoms of Huntington's disease. In certain embodiments administration of compounds targeted to huntingtin as described herein may improve the symptoms of Huntington's disease as measured by any metric known to those having skill in the art. In certain embodiments, administration of compounds targeted to huntingtin as described herein may improve a rodent's rotaraod assay performance. In certain embodiments, administration of compounds targeted to huntingtin as described herein may improve a rodent's plus maze assay. In certain embodiments, administration of compounds targeted to huntingtin as described herein may improve a rodent's open field assay performance.

Accordingly, provided herein are methods for ameliorating a symptom associated with Huntington's disease in a subject in need thereof. In certain embodiments, provided is a method for reducing the rate of onset of a symptom associated with Huntington's disease. In certain embodiments, provided is a method for reducing the severity of a symptom associated with Huntington's disease. In certain embodiments, provided is a method for regenerating neurological function as shown by an improvement of a symptom associated with Huntington's disease. In such embodiments, the methods comprise administering to an individual or animal in need thereof a therapeutically effective amount of a compound targeted to a huntingtin nucleic acid.

Huntington's disease is characterized by numerous physical, neurological, psychiatric, and/or peripheral symptoms. Any symptom known to one of skill in the art to be associated with Huntington's disease can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the symptom is a physical symptom selected from the group consisting of restlessness, lack of coordination, unintentionally initiated motions, unintentionally uncompleted motions, unsteady gait, chorea, rigidity, writhing motions, abnormal posturing, instability, abnormal facial expressions, difficulty chewing, difficulty swallowing, difficulty speaking, seizure, and sleep disturbances. In certain embodiments, the symptom is a cognitive symptom selected from the group consisting of impaired planning, impaired flexibility, impaired abstract thinking, impaired rule acquisition, impaired initiation of appropriate actions, impaired inhibition of inappropriate actions, impaired short-term memory, impaired long-term memory, paranoia, disorientation, confusion, hallucination and dementia. In certain embodiments, the symptom is a psychiatric symptom selected from the group consisting of anxiety, depression, blunted affect, egocentrisms, aggression, compulsive behavior, irritability and suicidal ideation. In certain embodiments, the symptom is a peripheral symptom selected from the group consisting of reduced brain mass, muscle atrophy, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, and testicular atrophy.

In certain embodiments, the symptom is restlessness. In certain embodiments, the symptom is lack of coordination. In certain embodiments, the symptom is unintentionally initiated motions. In certain embodiments, the symptom is unintentionally uncompleted motions. In certain embodiments, the symptom is unsteady gait. In certain embodiments, the symptom is chorea. In certain embodiments, the symptom is rigidity. In certain embodiments, the symptom is writhing motions. In certain embodiments, the symptom is abnormal posturing. In certain embodiments, the symptom is instability. In certain embodiments, the symptom is abnormal facial expressions. In certain embodiments, the symptom is difficulty chewing. In certain embodiments, the symptom is difficulty swallowing. In certain embodiments, the symptom is difficulty speaking. In certain embodiments, the symptom is seizures. In certain embodiments, the symptom is sleep disturbances.

In certain embodiments, the symptom is impaired planning. In certain embodiments, the symptom is impaired flexibility. In certain embodiments, the symptom is impaired abstract thinking. In certain embodiments, the symptom is impaired rule acquisition. In certain embodiments, the symptom is impaired initiation of appropriate actions. In certain embodiments, the symptom is impaired inhibition of inappropriate actions. In certain embodiments, the symptom is impaired short-term memory. In certain embodiments, the symptom is impaired long-term memory. In certain embodiments, the symptom is paranoia. In certain embodiments, the symptom is disorientation. In certain embodiments, the symptom is confusion. In certain embodiments, the symptom is hallucination. In certain embodiments, the symptom is dementia.

In certain embodiments, the symptom is anxiety. In certain embodiments, the symptom is depression. In certain embodiments, the symptom is blunted affect. In certain embodiments, the symptom is egocentrism. In certain embodiments, the symptom is aggression. In certain embodiments, the symptom is compulsive behavior. In certain embodiments, the symptom is irritability. In certain embodiments, the symptom is suicidal ideation.

In certain embodiments, the symptom is reduced brain mass. In certain embodiments, the symptom is muscle atrophy. In certain embodiments, the symptom is cardiac failure. In certain embodiments, the symptom is impaired glucose tolerance. In certain embodiments, the symptom is weight loss. In certain embodiments, the symptom is osteoporosis. In certain embodiments, the symptom is testicular atrophy.

In certain embodiments, symptoms of Huntington's disease may be quantifiable. For example, osteoporosis may be measured and quantified by, for example, bone density scans. For such symptoms, in certain embodiments, the symptom may be reduced by about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.

In certain embodiments, provided are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has Huntington's disease.

In certain embodiments, administration of an antisense compound targeted to a huntingtin nucleic acid results in reduction of huntingtin expression by at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.

In certain embodiments, pharmaceutical compositions comprising an antisense compound targeted to huntingtin are used for the preparation of a medicament for treating a patient suffering or susceptible to Huntington's disease.

F. Certain Pharmaceutical Compositions

In certain embodiments, the present invention provides pharmaceutical compositions comprising one or more antisense compound. In certain embodiments, such pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutical composition comprises a sterile saline solution and one or more antisense compound. In certain embodiments, such pharmaceutical composition consists of a sterile saline solution and one or more antisense compound. In certain embodiments, the sterile saline is pharmaceutical grade saline. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and sterile water. In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile water. In certain embodiments, the sterile saline is pharmaceutical grade water. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and phosphate-buffered saline (PBS). In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile phosphate-buffered saline (PBS). In certain embodiments, the sterile saline is pharmaceutical grade PBS.

In certain embodiments, antisense compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.

Pharmaceutical compositions comprising antisense compounds encompass any pharmaceutically acceptable salts, esters, or salts of such esters. In certain embodiments, pharmaceutical compositions comprising antisense compounds comprise one or more oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of antisense compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.

A prodrug can include the incorporation of additional nucleosides at one or both ends of an oligomeric compound which are cleaved by endogenous nucleases within the body, to form the active antisense oligomeric compound.

Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.

In certain embodiments, pharmaceutical compositions provided herein comprise one or more modified oligonucleotides and one or more excipients. In certain such embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.

In certain embodiments, a pharmaceutical composition provided herein comprises a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.

In certain embodiments, a pharmaceutical composition provided herein comprises one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.

In certain embodiments, a pharmaceutical composition provided herein comprises a co-solvent system. Certain of such co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. In certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80™ and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80™; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.

In certain embodiments, a pharmaceutical composition provided herein is prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration.

In certain embodiments, a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, etc.). In certain of such embodiments, a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. In certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives).

In certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multi-dose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes. Aqueous injection suspensions may contain.

G. Administration

In certain embodiments, the compounds and compositions as described herein are administered parenterally.

In certain embodiments, parenteral administration is by infusion. Infusion can be chronic or continuous or short or intermittent. In certain embodiments, infused pharmaceutical agents are delivered with a pump. In certain embodiments, parenteral administration is by injection.

In certain embodiments, compounds and compositions are delivered to the CNS. In certain embodiments, compounds and compositions are delivered to the cerebrospinal fluid. In certain embodiments, compounds and compositions are administered to the brain parenchyma. In certain embodiments, compounds and compositions are delivered to an animal by intrathecal administration, or intracerebroventricular administration. Broad distribution of compounds and compositions, described herein, within the central nervous system may be achieved with intraparenchymal administration, intrathecal administration, or intracerebroventricular administration.

In certain embodiments, parenteral administration is by injection. The injection may be delivered with a syringe or a pump. In certain embodiments, the injection is a bolus injection. In certain embodiments, the injection is administered directly to a tissue, such as striatum, caudate, cortex, hippocampus and cerebellum.

Therefore, in certain embodiments, delivery of a compound or composition described herein can affect the pharmacokinetic profile of the compound or composition. In certain embodiments, injection of a compound or composition described herein, to a targeted tissue improves the pharmacokinetic profile of the compound or composition as compared to infusion of the compound or composition. In a certain embodiment, the injection of a compound or composition improves potency compared to broad diffusion, requiring less of the compound or composition to achieve similar pharmacology. In certain embodiments, similar pharmacology refers to the amount of time that a target mRNA and/or target protein is down-regulated (e.g. duration of action). In certain embodiments, methods of specifically localizing a pharmaceutical agent, such as by bolus injection, decreases median effective concentration (EC50) by a factor of about 50 (e.g. 50 fold less concentration in tissue is required to achieve the same or similar pharmacodynamic effect). In certain embodiments, methods of specifically localizing a pharmaceutical agent, such as by bolus injection, decreases median effective concentration (EC50) by a factor of 20, 25, 30, 35, 40, 45 or 50. In certain embodiments the pharmaceutical agent in an antisense compound as further described herein. In certain embodiments, the targeted tissue is brain tissue. In certain embodiments the targeted tissue is striatal tissue. In certain embodiments, decreasing EC50 is desirable because it reduces the dose required to achieve a pharmacological result in a patient in need thereof.

In certain embodiments, an antisense oligonucleotide is delivered by injection or infusion once every month, every two months, every 90 days, every 3 months, every 6 months, twice a year or once a year.

H. Certain Combination Therapies

In certain embodiments, one or more pharmaceutical compositions are co-administered with one or more other pharmaceutical agents. In certain embodiments, such one or more other pharmaceutical agents are designed to treat the same disease, disorder, or condition as the one or more pharmaceutical compositions described herein. In certain embodiments, such one or more other pharmaceutical agents are designed to treat a different disease, disorder, or condition as the one or more pharmaceutical compositions described herein. In certain embodiments, such one or more other pharmaceutical agents are designed to treat an undesired side effect of one or more pharmaceutical compositions as described herein. In certain embodiments, one or more pharmaceutical compositions are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent. In certain embodiments, one or more pharmaceutical compositions are co-administered with another pharmaceutical agent to produce a combinational effect. In certain embodiments, one or more pharmaceutical compositions are co-administered with another pharmaceutical agent to produce a synergistic effect.

In certain embodiments, one or more pharmaceutical compositions and one or more other pharmaceutical agents are administered at the same time. In certain embodiments, one or more pharmaceutical compositions and one or more other pharmaceutical agents are administered at different times. In certain embodiments, one or more pharmaceutical compositions and one or more other pharmaceutical agents are prepared together in a single formulation. In certain embodiments, one or more pharmaceutical compositions and one or more other pharmaceutical agents are prepared separately.

In certain embodiments, pharmaceutical agents that may be co-administered with a pharmaceutical composition of include antipsychotic agents, such as, e.g., haloperidol, chlorpromazine, clozapine, quetapine, and olanzapine; antidepressant agents, such as, e.g., fluoxetine, sertraline hydrochloride, venlafaxine and nortriptyline; tranquilizing agents such as, e.g., benzodiazepines, clonazepam, paroxetine, venlafaxin, and beta-blockers; mood-stabilizing agents such as, e.g., lithium, valproate, lamotrigine, and carbamazepine; paralytic agents such as, e.g., Botulinum toxin; and/or other experimental agents including, but not limited to, tetrabenazine (Xenazine), creatine, conezyme Q10, trehalose, docosahexanoic acids, ACR16, ethyl-EPA, atomoxetine, citalopram, dimebon, memantine, sodium phenylbutyrate, ramelteon, ursodiol, zyprexa, xenasine, tiapride, riluzole, amantadine, [123I]MNI-420, atomoxetine, tetrabenazine, digoxin, detromethorphan, warfarin, alprozam, ketoconazole, omeprazole, and minocycline.

Nonlimiting Disclosure and Incorporation by Reference

While certain compounds, compositions and methods described herein have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the compounds described herein and are not intended to limit the same. Each of the references, GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.

Although the sequence listing accompanying this filing identifies each sequence as either “RNA” or “DNA” as required, in reality, those sequences may be modified with any combination of chemical modifications. One of skill in the art will readily appreciate that such designation as “RNA” or “DNA” to describe modified oligonucleotides is, in certain instances, arbitrary. For example, an oligonucleotide comprising a nucleoside comprising a 2′-OH sugar moiety and a thymine base could be described as a DNA having a modified sugar (2′-OH for the natural 2′-H of DNA) or as an RNA having a modified base (thymine (methylated uracil) for natural uracil of RNA).

Accordingly, nucleic acid sequences provided herein, including, but not limited to those in the sequence listing, are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases. By way of further example and without limitation, an oligomeric compound having the nucleobase sequence “ATCGATCG” encompasses any oligomeric compounds having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and oligomeric compounds having other modified or naturally occurring bases, such as “AT^(me)CGAUCG,” wherein ^(me)C indicates a cytosine base comprising a methyl group at the 5-position.

EXAMPLES

The following examples illustrate certain embodiments of the present invention and are not limiting. Moreover, where specific embodiments are provided, the inventors have contemplated generic application of those specific embodiments. For example, disclosure of an oligonucleotide having a particular motif provides reasonable support for additional oligonucleotides having the same or similar motif. And, for example, where a particular high-affinity modification appears at a particular position, other high-affinity modifications at the same position are considered suitable, unless otherwise indicated.

To allow assessment of the relative effects of nucleobase sequence and chemical modification, throughout the examples, oligomeric compounds are assigned a “Sequence Code.” Oligomeric compounds having the same Sequence Code have the same nucleobase sequence. Oligomeric compounds having different Sequence Codes have different nucleobase sequences.

Example 1 Single Nucleotide Polymorphisms (SNPs) in the Huntingtin (HTT) Gene Sequence

SNP positions (identified by Hayden et al, WO/2009/135322) associated with the HTT gene were mapped to the HTT genomic sequence, designated herein as SEQ ID NO: 1 (NT_006081.18 truncated from nucleotides 1566000 to 1768000). Table 15 provides SNP positions associated with the HTT gene. Table 15 provides a reference SNP ID number from the Entrez SNP database at the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp), incorporated herein by reference. Table 15 furnishes further details on each SNP. The ‘Reference SNP ID number’ or ‘RS number’ is the number designated to each SNP from the Entrez SNP database at NCBI, incorporated herein by reference. ‘SNP position’ refers to the nucleotide position of the SNP on SEQ ID NO: 1. ‘Polymorphism’ indicates the nucleotide variants at that SNP position. ‘Major allele’ indicates the nucleotide associated with the major allele, or the nucleotide present in a statistically significant proportion of individuals in the human population. ‘Minor allele’ indicates the nucleotide associated with the minor allele, or the nucleotide present in a relatively small proportion of individuals in the human population.

TABLE 15 Single Nuclear Polymorphisms (SNPs) and their positions on SEQ ID NO: 1 SNP Major Minor RS No. position Polymorphism allele allele rs2857936 1963 C/T C T rs12506200 3707 A/G G A rs762855 14449 A/G G A rs3856973 19826 G/A G A rs2285086 28912 G/A A G rs7659144 37974 C/G C G rs16843804 44043 C/T C T rs2024115 44221 G/A A G rs10015979 49095 A/G A G rs7691627 51063 A/G G A rs2798235 54485 G/A G A rs4690072 62160 G/T T G rs6446723 66466 C/T T C rs363081 73280 G/A G A rs363080 73564 T/C C T rs363075 77327 G/A G A rs363064 81063 T/C C T rs3025849 83420 A/G A G rs6855981 87929 A/G G A rs363102 88669 G/A A G rs11731237 91466 C/T C T rs4690073 99803 A/G G A rs363144 100948 T/G T G rs3025838 101099 C/T C T rs34315806 101687 A/G G A rs363099 101709 T/C C T rs363096 119674 T/C T C rs2298967 125400 C/T T C rs2298969 125897 A/G G A rs6844859 130139 C/T T C rs363092 135682 C/A C A rs7685686 146795 A/G A G rs363088 149983 A/T A T rs362331 155488 C/T T C rs916171 156468 G/C C G rs362322 161018 A/G A G rs362275 164255 T/C C T rs362273 167080 A/G A G rs2276881 171314 G/A G A rs3121419 171910 T/C C T rs362272 174633 G/A G A rs362271 175171 G/A G A rs3775061 178407 C/T C T rs362310 179429 A/G G A rs362307 181498 T/C C T rs362306 181753 G/A G A rs362303 181960 T/C C T rs362296 186660 C/A C A rs1006798 198026 A/G A G

Example 2 Modified Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

A series of modified oligonucleotides were designed based on the parent gapmer, ISIS 460209 wherein the central gap region contains nine 2′-deoxyribonucleosides. These modified oligonucleotides were designed by introducing various chemical modifications in the central gap region and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting rs7685686 while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to the parent gapmer, ISIS 460209.

The modified oligonucleotides were created with a 3-9-3 motif and are described in Table 16. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are 3-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e”, “k”, “y”, or “z” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt), a subscript “y” indicates an α-L-LNA bicyclic nucleoside and a subscript “z” indicates a F-HNA modified nucleoside. ^(P)U indicates a 5-propyne uridine nucleoside and ^(x)T indicates a 2-thio-thymidine nucleoside.

The number in parentheses indicates the position on the modified oligonucleotide opposite to the SNP position, as counted from the 5′-terminus.

Cell Culture and Transfection

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented below.

Analysis of IC₅₀'s

The half maximal inhibitory concentration (IC₅₀) of each oligonucleotide is presented in Table 17 and was calculated by plotting the concentrations of oligonucleotides used versus the percent inhibition of HTT mRNA expression achieved at each concentration, and noting the concentration of oligonucleotide at which 50% inhibition of HTT mRNA expression was achieved compared to the control. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

The parent gapmer, ISIS 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the activity and selectivity of the modified oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 17, modified oligonucleotides having chemical modifications in the central gap region at the SNP position exhibited similar activity with an increase in selectivity comparing to the parent gapmer, wherein the central gap region contains full deoxyribonucleosides.

TABLE 16 Modified oligonucleotides targeting HTT rs7685686 Wing chemistry SEQ ID ISIS NO Sequence (5′ to 3 ) Gap chemistry 5′ 3′ NO. 460209* (8) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) Full Deoxy ekk kke 10 539560 (8) T_(e)A_(k)A_(k)ATTG^(p)UCATCA_(k)C_(k)C_(e) Deoxy/5-Propyne ekk kke 11 539563 (8) T_(e)A_(k)A_(k)ATTG^(x)TCATCA_(k)C_(k)C_(e) Deoxy/2-Thio ekk kke 10 539554 (8) T_(e)A_(k)A_(k)ATTGU_(y)CATCA_(k)C_(k)C_(e) Deoxy/α-L-LNA ekk kke 11 542686 (8) T_(e)A_(k)A_(k)ATTGT_(z)CATCA_(k)C_(k)C_(e) Deoxy/F-HNA ekk kke 10 e = 2′-MOE, k = cEt

TABLE 17 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells Mut IC₅₀ Wt IC₅₀ Selectivity Wing chemistry ISIS NO (μM) (μM) (mut vs wt) Gap chemistry 5′ 3′ 460209* (8)  0.41 2.0 4.9 Full Deoxy ekk kke 539560 (8) 0.29 1.1 3.8 Deoxy/5-Propyne ekk kke 539563 (8) 0.45 3.1 6.9 Deoxy/2-Thio ekk kke 539554 (8) 3.5 >10 >3 Deoxy/α-L-LNA ekk kke 542686 (8) 0.5 3.1 6.0 Deoxy/F-HNA ekk kke

Example 3 Modified Oligonucleotides Comprising Chemical Modifications in the Gap Region Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional modified oligonucleotides were designed in a similar manner as the antisense oligonucleotides described in Table 16. Various chemical modifications were introduced in the central gap region at the SNP position in an effort to improve selectivity while maintaining activity in reducing mutant HTT mRNA levels.

The modified oligonucleotides were created with a 3-9-3 motif and are described in Table 18. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are 3-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “a”, “e”, “f”, “h”, “k”, “1”, “R”, “w” are sugar modified nucleosides. A subscript “a” indicates a 2′-(ara)-F modified nucleoside, a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, a subscript “f” indicates a 2′-F modified nucleoside, a subscript “h” indicates a HNA modified nucleoside, a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt), a subscript “l” indicates a LNA modified nucleoside, a subscript “R” indicates a 5′-(R)-Me DNA, a subscript “w” indicates an unlocked nucleic acid (UNA) modified nucleoside. ^(a)T indicates an N3-ethylcyano thymidine nucleoside and ^(b)N indicates an abasic nucleoside (e.g. 2′-deoxyribonucleoside comprising a H in place of a nucleobase). Underlined nucleoside or the number in parentheses indicates the position on the modified oligonucleotide opposite to the SNP position, as counted from the 5′-terminus.

Thermal Stability Assay

The modified oligonucleotides were evaluated in thermal stability (T_(m)) assay. The T_(m)'s were measured using the method described herein. A Cary 100 Bio spectrophotometer with the Cary Win UV Thermal program was used to measure absorbance vs. temperature. For the T_(m) experiments, oligonucleotides were prepared at a concentration of 8 μM in a buffer of 100 mM Na+, 10 mM phosphate, 0.1 mM EDTA, pH 7. Concentration of oligonucleotides were determined at 85° C. The oligonucleotide concentration was 4 μM with mixing of equal volumes of test oligonucleotide and mutant or wild-type RNA strand. Oligonucleotides were hybridized with the mutant or wild-type RNA strand by heating duplex to 90° C. for 5 min and allowed to cool at room temperature. Using the spectrophotometer, T_(m) measurements were taken by heating duplex solution at a rate of 0.5 C/min in cuvette starting @ 15° C. and heating to 85° C. T_(m) values were determined using Vant Hoff calculations (A₂₆₀ vs temperature curve) using non self-complementary sequences where the minimum absorbance which relates to the duplex and the maximum absorbance which relates to the non-duplex single strand are manually integrated into the program.

Presented in Table 19 is the T_(m) for the modified oligonucleotides when duplexed to mutant or wild-type RNA complement. The T_(m) of the modified oligonucleotides duplexed with mutant RNA complement is denoted as “T_(m) (° C.) mut”. The T_(m) of the modified oligonucleotides duplexed with wild-type RNA complement is denoted as “T_(m) (° C.) wt”.

Cell Culture, Transfection and Selectivity Analysis

The modified oligonucleotides were also tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 19 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity as was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels.

The parent gapmer, ISIS 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the selectivity of the modified oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 19, improvement in selectivity was observed for antisense oligonucleotides comprising chemical modifications in the central gap region at the SNP site such as 5′-(R)-Me (ISIS 539558), HNA (ISIS 539559), and 2′-(ara)-F (ISIS 539565) in comparison to the parent full deoxy gapmer, ISIS 460209. Modified oligonucleotides comprising LNA (ISIS 539553) or 2′-F (ISIS 539570) showed comparable selectivity while UNA modification (ISIS 539556 or 543909) showed no selectivity. Modified oligonucleotides comprising modified nucleobase, N3-ethylcyano (ISIS 539564) or abasic nucleobase (ISIS 543525) showed little to no improvement in selectivity.

TABLE 18 Modified oligonucleotides comprising chemical modifications in the central gap region Wing SEQ chemistry ID ISIS NO Sequence (5′ to 3′) Gap chemistry 5′ 3′ NO. 460209* (8) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) Full Deoxy ekk kke 10 539553 (8) T_(e)A_(k)A_(k)ATTGT_(l) CATCA_(k)C_(k)C_(e) Deoxy/LNA ekk kke 10 539556 (8) T_(e)A_(k)A_(k)ATTGU_(w) CATCA_(k)C_(k)C_(e) Deoxy/UNA ekk kke 11 539558 (8) T_(e)A_(k)A_(k)ATTGT_(R) CATCA_(k)C_(k)C_(e) Deoxy/5′-(R)-Me DNA ekk kke 10 539559 (8) T_(e)A_(k)A_(k)ATTGT _(h) CATCA_(k)C_(k)C_(e) Deoxy/HNA ekk kke 10 539564 (8) T_(e)A_(k)A_(k)ATTG ^(n)TCATCA_(k)C_(k)C_(e) Deoxy/deoxy with N3- ekk kke 10 Ethylcyano nucleobase 539565 (8) T_(e)A_(k)A_(k)ATTGT_(a) CATCA_(k)C_(k)C_(e) Deoxy/2′-(ara)-F ekk kke 10 539570 (8) T_(e)A_(k)A_(k)ATTGT_(f) CATCA_(k)C_(k)C_(e) Deoxy/2′-F ekk kke 10 543525 (8) T_(e)A_(k)A_(k)ATTG ^(b)NCATCA_(k)C_(k)C_(e) Deoxy/Deoxy-Abasic ekk kke 12 543909 (5) T_(e)A_(k)A_(k)AU_(w) TGTCATCA_(k)C_(k)C_(e) Deoxy/UNA ekk kke 13 e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 19 Comparison of selectivity in inhibition of HTT mRNA levels and Tm of modified oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells Tm (° C.) % UTC Selectivity Wing chemistry ISIS NO mutant wt mutant wt (wt vs mut) Gap chemistry 5′ 3′ 460209* (8)  53.7 52.2 23 57 2.4 Full Deoxy ekk kke 539553 (8) 57.7 55.3 54 102 1.9 Deoxy/LNA ekk kke 539556 (8) 43.7 44.1 90 105 1.2 Deoxy/UNA ekk kke 539558 (8) 51.2 49.7 25 83 3.3 Deoxy/5′-(R)-Me DNA ekk kke 539559 (8) 55.4 50.5 18 62 3.5 Deoxy/HNA ekk kke 539564 (8) 42.8 43.1 86 135 1.6 Deoxy/Deoxy N3- ekk kke ethylcyano nucleobase 539565 (8) 53.8 52.5 14 46 3.4 Deoxy/2′-(ara)-F ekk kke 539570 (8) 54.4 51.8 25 50 2.0 Deoxy/2′-F ekk kke 543525 (8) 43.1 43.8 87 97 1.1 Deoxy/Deoxy Abasic ekk kke 543909 (5) 44.7 42.1 68 79 1.2 Deoxy/UNA ekk kke e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 4 Chimeric Oligonucleotides Comprising Self-Complementary Regions Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Chimeric oligonucleotides were designed based on the parent gapmer, ISIS 460209. These gapmers comprise self-complementary regions flanking the central gap region, wherein the central gap region contains nine deoxyribonucleosides and the self-complementary regions are complementary to one another. The underlined nucleosides indicate the portion of the 5′-end that is self-complement to the portion of the 3′-end.

The gapmers and their motifs are described in Table 20. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 21 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of the mutant HTT mRNA levels.

The parent gapmer, ISIS 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the selectivity of the modified oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 21, improvement in selectivity was observed for chimeric oligonucleotides comprising 5-9-5 (ISIS 550913), 6-9-6 (ISIS 550912), 6-9-3 (ISIS 550907) or 3-9-7 (ISIS 550904) in comparison to the parent gapmer motif, 3-9-3 (ISIS 460209). The remaining gapmers showed moderate to little improvement in selectivity.

TABLE 20 Chimeric oligonucleotides comprising various wing motifs targeted to HTT rs7685686 Wing chemistry SEQ ID ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 544838 T_(e) A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) A_(k) 3-9-4 ekk kkek 14 544840 T_(e)A_(k)A_(k) ATTGTCATCA_(k)C_(k)C_(e) T_(k)T_(k)A_(k) 3-9-6 ekk kkekkk 15 544842 T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) A_(k)T_(k)T_(k)T_(k)A_(k) 3-9-8 ekk kkekkkkk 16 550903 T_(e)A_(k)A_(k) ATTGTCATCA_(k)C_(k)C_(e) T_(k)A_(k) 3-9-5 ekk kkekk 17 550904 T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) T_(k)T_(k)T_(k)A_(k) 3-9-7 ekk kkekkkk 18 550905 G_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k) C_(e) 4-9-3 kekk kke 19 550906 G_(k)G_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k) C_(k)C_(e) 5-9-3 kkekk kke 20 550907 G_(k)G_(k)T _(k)T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 6-9-3 kkkekk kke 21 550908 G_(k)G_(k)T_(k)G_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 7-9-3 kkkkekk kke 22 550909 G_(k)G_(k)T_(k)G_(k)A_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 8-9-3 kkkkkekk kke 23 550910 G_(k)G_(k)C_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) G_(k)C_(k)C_(k) 6-9-6 kkkekk kkekkk 24 550911 G_(k)C_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) G_(k)C_(k) 5-9-5 kkekk kkekk 25 550912 T_(k)A_(k)A_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) T_(k)T_(k)A_(k) 6-9-6 kkkekk kkekkk 26 550913 A_(k)A_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) T_(k)T_(k) 5-9-5 kkekk kkekk 27 550914 T_(k)C_(k)T_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) A_(k)G_(k)A_(k) 6-9-6 kkkekk kkekkk 28 550915 C_(k)T_(k) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) A_(k)G_(k) 5-9-5 kkekk kkekk 29 e = 2′-MOE, k = cEt

TABLE 21 Comparison of selectivity in inhibition of HTT mRNA levels of chimeric oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells % UTC Selectivity wing chemistry ISIS NO mut wt (wt vs. mut) Motif 5′ 3′ 460209* 23 57 2.4 3-9-3 ekk kke 544838 13 25 2.0 3-9-4 ekk kkek 544840 17 31 1.8 3-9-6 ekk kkekkk 544842 55 102 1.9 3-9-8 ekk kkekkkkk 550903 13 36 2.7 3-9-5 ekk kkekk 550904 23 67 3.0 3-9-7 ekk kkekkkk 550905 21 51 2.4 4-9-3 kekk kke 550906 23 67 2.9 5-9-3 kkekk kke 550907 30 93 3.1 6-9-3 kkkekk kke 550908 60 80 2.4 7-9-3 kkkkekk kke 550909 42 101 2.4 8-9-3 kkkkkekk kke 550910 57 102 1.8 6-9-6 kkkekk kkekkk 550911 18 40 2.2 5-9-5 kkekk kkekk 550912 14 51 3.6 6-9-6 kkkekk kkekkk 550913 8 36 4.5 5-9-5 kkekk kkekk 550914 29 45 1.5 6-9-6 kkkekk kkekkk 550915 13 28 2.1 5-9-5 kkekk kkekk e = 2′-MOE, k = cEt

Example 5 Chimeric Antisense Oligonucleotides Comprising Non-Self-Complementary Regions Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional gapmers are designed based on the most selective gapmers from studies described in Tables 61 and 62 (ISIS 550912 and 550913). These gapmers are created such that they cannot form self-structure in the effort to evaluate if the increased activity simply is due to higher binding affinity. Gapmers are designed by deleting two or three nucleotides at the 3′-terminus and are created with, 6-9-3 or 5-9-3 motif.

The chimeric oligonucleotides and their motifs are described in Table 22. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

The gapmers, ISIS 550912 and ISIS 550913, from which the newly designed gapmers are derived from, are marked with an asterisk (*) in the table.

TABLE 22 Non-self-complementary chimeric oligonucleotides targeting HTT SNP Wing chemistry SEQ ID ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ NO. 550912* T_(k)A_(k)A_(k)T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e)T_(k)T_(k)A_(k) 6-9-6 kkkekk kkekkk 26 550913* A_(k)A_(k)T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e)T_(k)T_(k) 5-9-5 kkekk kkekk 27 556879 T_(k)A_(k)A_(k)T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 6-9-3 kkkekk kke 30 556880 A_(k)A_(k)T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 5-9-3 kkekk kke 31 e = 2′-MOE, k = cEt

Example 6 Chimeric Oligonucleotides Containing Mismatches Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

A series of chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209, wherein the central gap region contains nine 2′-deoxyribonucleosides. These gapmers were designed by introducing modified nucleosides at both, 5′ and 3′ termini. Gapmers were also created with a single mismatch shifted slightly upstream and downstream (i.e. “microwalk”) within the central gap region and with the SNP position opposite position 5 of the parent gapmer, as counted from the 5′-gap terminus.

The gapmers and their motifs are described in Table 23. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Underlined nucleosides indicate the mismatch position, as counted from the 5′-gap terminus.

These gapmers were evaluated for thermal stability (T_(m)) using methods described in Example 3. Presented in Table 24 are the T_(m) measurements for chimeric antisense oligonucleotides when duplexed to mutant or wild-type RNA complement. The T_(m) of chimeric antisense oligonucleotides duplexed with mutant RNA complement is denoted as “T_(m) (° C.) mut”. The T_(m) of chimeric antisense oligonucleotides duplexed with wild-type RNA complement is denoted as “T_(m) (° C.) wt”.

These gapmers were also tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 24 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels.

The parent gapmer, ISIS 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the selectivity of the modified oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 24, improvement in selectivity was observed for gapmers comprising a 4-9-4 motif with a central deoxy gap region (ISIS 476333) or a single mismatch at position 8 within the gap region (ISIS 543531) in comparison to the parent gapmer. The remaining gapmers showed moderate to little improvement in selectivity.

TABLE 23 Chimeric oligonucleotides containing a single mismatch targeting mutant HTT SNP Wing Mismatch chemistry SEQ ISIS NO Sequence (5′ to 3′) position Motif 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) — 3-9-3 ekk kke 10 476333 A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) — 4-9-4 ekek keke 32 543526 A_(e)T_(k)A_(e)A_(k)ATTCTCATCA_(k)C_(e)C_(k)A_(e) 4 4-9-4 ekek keke 33 543527 A_(e)T_(k)A_(e)A_(k)ATAGTCATCA_(k)C_(e)C_(k)A_(e) 3 4-9-4 ekek keke 34 543529 A_(e)T_(k)A_(e)A_(k)ATTGTGATCA_(k)C_(e)C_(k)A_(e) 6 4-9-4 ekek keke 35 543530 A_(e)T_(k)A_(e)A_(k)ATTGTCTTCA_(k)C_(e)C_(k)A_(e) 7 4-9-4 ekek keke 36 543531 A_(e)T_(k)A_(e)A_(k)ATTGTCAACA_(k)C_(e)C_(k)A_(e) 8 4-9-4 ekk keke 37 543532 T_(e)A_(k)A_(k)ATTCTCATCA_(k)C_(k)C_(e) 4 3-9-3 ekk kke 38 543534 T_(e)A_(k)A_(k)AATGTCATCA_(k)C_(k)C_(e) 2 3-9-3 ekk kke 39 543535 T_(e)A_(k)A_(k)ATTGTGATCA_(k)C_(k)C_(e) 6 3-9-3 ekk kke 40 543536 T_(e)A_(k)A_(k)ATTGTCTTCA_(k)C_(k)C_(e) 7 3-9-3 ekk kke 41 543537 T_(e)A_(k)A_(k)ATTGTCAACA_(k)C_(k)C_(e) 8 3-9-3 ekk kke 42 e = 2′-MOE, k = cEt

TABLE 24 Comparison of selectivity and T_(m) of chimeric oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells Tm (° C.) % UTC Selectivity Mismatch Wing chemistry ISIS NO mut wt mut wt (wt vs mut) position Motif 5′ 3′  460209* 53.7 52.2 23 57 2.4 — 3-9-3 ekk kke 476333 60.2 58.4 10 37 3.6 — 4-9-4 ekek keke 543526 47.9 46.6 70 86 1.2 4 4-9-4 ekek keke 543527 52.6 49.9 40 103 2.6 3 4-9-4 ekek keke 543529 50.3 49.0 66 102 1.5 6 4-9-4 ekek keke 543530 52.9 50.9 67 110 1.6 7 4-9-4 ekek keke 543531 53.3 50.3 46 136 3.0 8 4-9-4 ekk keke 543532 43.6 42.8 127 151 1.2 4 3-9-3 ekk kke 543534 45.9 43.8 67 95 1.4 2 3-9-3 ekk kke 543535 44.0 43.3 96 113 1.2 6 3-9-3 ekk kke 543536 46.8 44.6 106 104 1.0 7 3-9-3 ekk kke 543537 45.9 44.3 77 81 1.1 8 3-9-3 ekk kke e = 2′-MOE, k = cEt

Example 7 Chimeric Oligonucleotides Comprising Mismatches Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides are designed based on two gapmers selected from studies described in Tables 64 and 65 (ISIS 476333 and ISIS 460209) wherein the central gap region contains nine 2′-deoxyribonucleosides. These gapmers are designed by introducing a single mismatch, wherein the mismatch will be shifted throughout the antisense oligonucleotide (i.e. “microwalk”). Gapmers are also created with, 4-9-4 or 3-9-3 motifs and with the SNP position opposite position 8 of the original gapmers, as counted from the 5′-terminus.

The gapmers and their motifs are described in Table 25. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Underlined nucleosides indicate the mismatch position, as counted from the 5′-terminus.

The gapmers, ISIS 476333 and ISIS 460209, in which the newly designed antisense oligonucleotides are derived from, are marked with an asterisk (*) in the table.

TABLE 25 Chimeric oligonucleotides comprising mismatches targeting HTT SNP Wing Mismatch chemistry SEQ ISIS NO Sequence (5′ to 3′) position Motif 5′ 3′ ID NO. 476333* A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) — 4-9-4 ekek keke 32 554209 T _(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) 1 4-9-4 ekek keke 43 554210 A_(e) A _(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) 2 4-9-4 ekek keke 44 554211 A_(e)T_(k) T _(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) 3 4-9-4 ekek keke 45 554212 A_(e)T_(k)A_(e) T _(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) 4 4-9-4 ekek keke 46 554213 A_(e)T_(k)A_(e)A_(k) TTTGTCATCA_(k)C_(e)C_(k)A_(e) 5 4-9-4 ekek keke 47 554214 A_(e)T_(k)A_(e)A_(k)ATTGTCATGA_(k)C_(e)C_(k)A_(e) 13 4-9-4 ekek keke 48 554215 A_(e)T_(k)A_(e)A_(k)ATTGTCATCT _(k)C_(e)C_(k)A_(e) 14 4-9-4 ekek keke 49 554216 A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k) G _(e)C_(k)A_(e) 15 4-9-4 ekek keke 50 554217 A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e) G _(k)A_(e) 16 4-9-4 ekek keke 51 554218 A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k) T _(e) 17 4-9-4 ekek keke 52 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) — 3-9-3 ekk kke 10 562481 T_(e)A_(k)A_(k) GTTGTCATCA_(k)C_(k)C_(e) 4 3-9-3 ekk kke 53 554482 T_(e)A_(k)A_(k)AGTGTCATCA_(k)C_(k)C_(e) 5 3-9-3 ekk kke 54 554283 T_(e)A_(k)A_(k)ATGGTCATCA_(k)C_(k)C_(e) 6 3-9-3 ekk kke 55 e = 2′-MOE, k = cEt

Example 8 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209, wherein the central gap region contains nine 2′-deoxyribonucleosides. These gapmers were designed by shortening the central gap region to seven 2′-deoxyribonuclosides. Gapmers were also created with, 5-7-5 motif and with the SNP position opposite position 8 or 9 of the parent gapmer, as counted from the 5′-terminus.

The gapmers and their motifs are described in Table 26. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Underlined nucleoside or the number in parentheses indicates the position on the modified oligonucleotide opposite to the SNP position, as counted from the 5′-terminus.

The chimeric antisense oligonucleotides were tested in vitro. ISIS 141923 was included in the study as a negative control and is denoted as “neg control”. A non-allele specific antisense oligonucleotide, ISIS 387916 was used as a positive control and is denoted as “pos control”. ISIS 460209 was included in the study for comparison. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3, and 10 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 27.

The IC₅₀ and selectivity were calculated using methods described previously in Example 2. As illustrated in Table 27, no improvement in potency and selectivity was observed for the chimeric antisense oligonucleotides as compared to ISIS 460209.

TABLE 26 Chimeric antisense oligonucleotides targeting HTT rs7685686 Wing Chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ ID NO. 460209* (8) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 460085 (9) A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeeee eeeee 32 540108 (9) A_(e)T_(e)A_(e)A_(k)A_(k)TTGTCATC_(k)A_(k)C_(e)C_(e)A_(e) 5-7-5 eeekk kkeee 32 387916 T_(e)C_(e)T_(e)C_(e)T_(e)ATTGCACATTC_(e)C_(e)A_(e)A_(e)G_(e) 5-10-5 eeeee eeeee 56 (pos control) 141923 C_(e)C_(e)T_(e)T_(e)C_(e)CCTGAAGGTTC_(e)C_(e)T_(e)C_(e)C_(e) 5-10-5 eeeee eeeee 57 (neg control) e = 2′-MOE, k = cEt

TABLE 27 Comparison of inhibition of HTT mRNA levels and selectivity of chimeric antisense oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells Mut IC₅₀ Wt IC₅₀ Selectivity Wing chemistry ISIS NO (μM) (μM) (mut vs wt) Motif 5′ 3′ 460209* (8)  0.41 2.0 4.9 3-9-3 ekk kke 460085 (9) 3.5 >10 >3 5-7-5 eeeee eeeee 540108 (9) 0.41 — — 5-7-5 eeekk kkeee 387916 0.39 0.34 1.0 5-10-5 eeeee eeeee (pos control) 141923 >10 >10 — 5-10-5 eeeee eeeee (neg control) e = 2′-MOE, k = cEt

Example 9 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209, wherein the central gap region contains nine 2′-deoxyribonucleosides. These gapmers were designed with the central gap region shortened or interrupted by introducing various modifications either within the gap or by adding one or more modified nucleosides to the 3′-most 5′-region or to the 5′-most 3′-region. Gapmers were created with the SNP position opposite position 8 of the parent gapmer, as counted from the 5′-terminus.

The gapmers and their motifs are described in Table 28. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

The chimeric antisense oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 29 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels. ISIS 460209 marked with an asterisk (*) in the table was included in the study for comparison.

As illustrated in Table 29, modifications to the 3′-most 5′-region nucleosides that shorten the gap from 9 to 7 or 8 nucleotides (ISIS 551429 and ISIS 551426) improved selectivity and potency comparing to the parent gapmer (ISIS 460209). The remaining chimeric antisense oligonucleotides showed moderate to little improvement in selectivity.

TABLE 28 Short-gap antisense oligonucleotides targeting HTT rs7685686 Wing Chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 551426 T_(e)A_(k)A_(e)A_(k)TTGTCATCA_(k)C_(k)C_(e) 4-8-3 ekek kke 10 551427 T_(e)A_(k)A_(e)AT_(k)TGTCATCA_(k)C_(k)C_(e) 3-9-3 or eke or kke 10 5-7-3 ekedk 551428 T_(e)A_(k)A_(e)ATT_(k)GTCATCA_(k)C_(k)C_(e) 3-9-3 or eke or kke 10 6-6-3 ekeddk 551429 T_(e)A_(e)A_(e)A_(k)T_(k)TGTCATCA_(k)C_(k)C_(e) 5-7-3 eeekk kke 10 e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 29 Comparison of selectivity in inhition of HTT mRNA levels of antisense oligonucleotides with ISIS 460209 targeted to rs7685686 in GM4022 cells % UTC Selectivity Wing chemistry ISIS NO mut wt (wt vs. mut) Motif 5′ 3′  460209* 23 57 2.4 3-9-3 ekk kke 551426 14 66 4.8 4-8-3 ekek kke 551427 35 97 2.8 3-9-3 or eke or ekedk kke 5-7-3 551428 61 110 1.8 3-9-3 or eke or ekeddk kke 6-6-3 551429 19 94 5.0 5-7-3 eeekk kke e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 10 Modified Oligonucleotides Targeting HTT SNP

A series of modified antisense oligonucleotides are designed based on the parent gapmer, ISIS 460209, wherein the central gap region contains nine 2′-deoxynucleosides and is marked with an asterisk (*) in the table. These modified oligonucleotides are designed by shortening or interrupting the gap with a single mismatch or various chemical modifications within the central gap region. The modified oligonucleotides are created with the SNP position opposite position 8 of the parent gapmer, as counted from the 5′-terminus.

The gapmers and their motifs are described in Table 30. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages, except for the internucleoside linkage with a subscript “p”, “pz” or “pw”. Subscript “p” indicates methyl phosphonate internucleoside linkage. Subscript “pz” indicates (R)-methyl phosphonate internucleoside linkage. Subscript “pw” indicates (S)-methyl phosphonate internucleoside linkage. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. ^(x)T indicates a 2-thio thymidine nucleoside. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e”, “k” or “b” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt) and a subscript “b” indicates a 5′-Me DNA modified nucleoside. Underlined nucleosides indicate the position of modification. Bold and underlined nucleosides indicate the mismatch position

TABLE 30 Short-gap chimeric oligonucleotides targeting HTT SNP Wing Sequence Chemistry ISIS NO (5′ to 3′) Motif Gap Chemistry 5′ 3′ SEQ ID NO. 460209* T_(e)A_(k)A_(k)ATTGTC 3-9-3 —  ekk  kke 10 ATCA_(k)C_(k)C_(e) XXXX16 T_(e)A_(k)A_(k)A ^(x) TTGT 3-9-3 Deoxy/2-thio ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX17 T_(e)A_(k)A_(k)AT ^(x) TGT 3-9-3 Deoxy/2-thio ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX18 T_(e)A_(k)A_(k)A ^(x) T ^(x) TGT 3-9-3 Deoxy/2-thio ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX19 T_(e)A_(k)A_(k)ATT _(p) GT 3-9-3 Deoxy/Methyl ekk kke 10 (558257) CATCA_(k)C_(k)C_(e) phosphonate XXXX20 T_(e)A_(k)A_(k)AT _(p) TGT 3-9-3 Deoxy/Methyl ekk kke 10 (558256) CATCA_(k)C_(k)C_(e) phosphonate XXXX20a T_(e)A_(k)A_(k)AT _(pz) TGT 3-9-3 Deoxy/(R)- ekk kke 10 CATCA_(k)C_(k)C_(e) Methyl phosphonate XXXX20b T_(e)A_(k)A_(k)AT _(pw) TG 3-9-3 Deoxy/(S)- ekk kke 10 TCATCA_(k)C_(k)C_(e) Methyl phosphonate XXXX21 T_(e)A_(k)A_(k) A _(p) TTGT 3-9-3 Methyl ekk kke 10 (558255) CATCA_(k)C_(k)C_(e) phosphonate XXXX22 T_(e)A_(k)A_(k)ATT _(b) GT 3-9-3 5′-Me-DNA ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX23 T_(e)A_(k)A_(k)AT _(b) TGT 3-9-3 5′-Me-DNA ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX24 T_(e)A_(k)A_(k) A _(b) TTGT 3-9-3 5′-Me-DNA ekk kke 10 CATCA_(k)C_(k)C_(e) XXXX25 T_(e)A_(k)A_(k) G TTGTC 4-8-3 Mismatch at ekk kke 53 ATCA_(k)C_(k)C_(e) position 4 XXXX26 T_(e)A_(k)A_(k)A G TGT 5-7-3 Mismatch at ekk kke 54 CATCA_(k)C_(k)C_(e) position 5 XXXX27 T_(e)A_(k)A_(k)AT G GT 6-6-3 Mismatch at ekk kke 55 CATCA_(k)C_(k)C_(e) position 6 e = 2′-MOE, k = cEt

Example 11 Short-Gap Chimeric Oligonucleotides Comprising Modifications at the Wing Regions Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209, wherein the central gap region contains nine 2′-deoxynucleosides. These gapmers were designed by shortening the central gap region to seven 2′-deoxynucleosides and introducing various modifications at the wing regions.

The gapmers and their motifs are described in Table 31. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

The number in parentheses indicates the position on the chimeric oligonucleotide opposite to the SNP position, as counted from the 5′-terminus.

These gapmers were evaluated for thermal stability (T_(m)) using methods described in Example 3. Presented in Table 32 is the T_(m) measurements for chimeric antisense oligonucleotides when duplexed to mutant or wild-type RNA complement. The T_(m) of chimeric antisense oligonucleotides duplexed with mutant RNA complement is denoted as “T_(m) (° C.) mut”. The T_(m) of chimeric antisense oligonucleotides duplexed with wild-type RNA complement is denoted as “T_(m) (° C.) wt”.

These gapmers were also tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 32 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels. ISIS 460209 marked with an asterisk (*) in the table was included in the study for comparison.

As illustrated in Table 32, improvement in selectivity was observed for gapmers comprising 2-7-8 or 5-7-5 motifs having cEt subunits at the wing regions in comparison to the parent gapmer, ISIS 460209. The remaining gapmers showed moderate to little improvement in selectivity.

TABLE 31 Short-gap chimeric oligonucleotides comprising wing modifications wing chemistry ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ SEQ ID NO. 460209* (8) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 540103 (6) A_(k)A_(k)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e)G_(e)A_(e)A_(e) 2-7-8 kk e8 58 540104 (6) A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e)G_(e)A_(e)A_(e) 2-7-8 ee e8 59 540105 (7) A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e)G_(e)A_(e) 3-7-7 eee e7 60 540106 (8) T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e)G_(e) 4-7-6 eeee e6 61 540107 (9) A_(e)T_(e)A_(e)A_(e)A_(k)TTGTCATC_(k)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeeek keeee 32 540109 (10) A_(e)A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e) 6-7-4 e6 e4 62 540110 (11) T_(e)A_(e)A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e) 7-7-3 e7 eee 63 540111 (12) T_(e)T_(e)A_(e)A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e) 8-7-2 e8 ee 64 540112 (12) T_(e)T_(e)A_(e)A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(k)A_(t) 8-7-2 e8 kk 64 e = 2′-MOE (e.g. e6 = eeeeee), and k = cEt

TABLE 32 Comparison of selectivity in inhibition of HTT mRNA levels of antisense oligonucleotides with ISIS 460209 targeted to RS7685686 in GM04022 cells Tm (° C.) % UTC Selectivity wing chemistry ISIS NO mut wt mut wt (wt vs mut) Motif 5′ 3′ 460209* (8)  53.7 52.2 23 57 2.4 3-9-3 ekk kke 540103 (6) 57.6 56.4 23 74 3.3 2-7-8 kk e8 540104 (6) 54.8 52.8 36 91 2.5 2-7-8 ee e8 540105 (7) 54.2 52.2 53 135 2.6 3-7-7 eee e7 540106 (8) 52.4 50.8 30 77 2.6 4-7-6 eeee e6 540107 (9) 56.6 54.7 19 62 3.3 5-7-5 eeeek keeee  540109 (10) 49.1 47.3 78 127 1.6 6-7-4 e6 e4  540110 (11) 42.8 41.2 89 112 1.3 7-7-3 e7 eee  540111 (12) 39.0 36.9 111 128 1.1 8-7-2 e8 ee  540112 (12) 44.2 42.4 86 102 1.2 8-7-2 e8 kk

Example 12

Chimeric Oligonucleotides with SNP Site Shifting within the Central Gap Region

Chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209 wherein the SNP site aligns with position 5 of the parent gapmer, as counted from the 5′-gap terminus. These gapmers were designed by shifting the SNP site upstream or downstream (i.e. microwalk) within the central gap region of the parent gapmer.

The gapmers and their motifs are described in Table 33. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Underline nucleosides indicate the position on the chimeric oligonucleotide aligns with the SNP site.

The SNP site indicates the position on the chimeric antisense oligonucleotide opposite to the SNP position, as counted from the 5′-gap terminus and is denoted as “SNP site”.

The chimeric oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. ISIS 460209 marked with an asterisk (*) in the table was included in the study for comparison.

The IC₅₀ and selectivity were calculated using the methods previously described in Example 2. As illustrated in Table 34, chimeric oligonucleotides comprising 4-9-2 (ISIS 540082) or 2-9-4 (ISIS 540095) motif with the SNP site at position 1 or 3 showed comparable activity and 2.5 fold selectivity as compared to their counterparts.

TABLE 33 Chimeric oligonucleotides designed by microwalk wing chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif SNP site 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 5 ekk kke 10 540082 A_(e)T_(k)T_(k)G_(k) TCATCACCAG_(k)A_(e) 4-9-2 1 ekkk ke 65 540089 T_(e)T_(k)A_(k)A_(k)TAAATTGTCA_(k)T_(e) 4-9-2 8 ekkk ke 66 540095 A_(e)T_(k)TGTCATCACC_(k)A_(k)G_(k)A_(e) 2-9-4 3 ek kkke 65 e = 2′-MOE, and k = cEt

TABLE 34 Comparison of inhibition of HTT mRNA levels and selectivity of chimeric oligonucleotides with ISIS 460209 targeted to HTT SNP Mut IC₅₀ Wt IC₅₀ Selectivity SNP Wing Chemistry ISIS NO (μM) (μM) (wt vs mut) Motif site 5′ 3′ 460209 0.41 2.0 4.9 3-9-3 5 ekk kke 540082 0.45 5.6 12 4-9-2 1 ekkk ke 540089 >10 >10 — 4-9-2 8 ekkk ke 540095 0.69 8.4 12 2-9-4 3 ek kkke e = 2′-MOE, and k = cEt

Example 13

Chimeric Oligonucleotides with SNP Site Shifting at Various Positions

Chimeric antisense oligonucleotides were designed based on the parent gapmer, ISIS 460209 wherein the SNP site aligns with position 8 of the parent gapmer, as counted from the 5′-terminus. These gapmers were designed by shifting the SNP site upstream or downstream (i.e. microwalk) of the original oligonucleotide.

The gapmers and their motifs are described in Table 35. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Underline nucleosides indicate the SNP site.

The SNP site indicates the position on the chimeric antisense oligonucleotide opposite to the SNP position, as counted from the 5′-terminus and is denoted as “SNP site”.

The chimeric oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. The results in Table 36 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels.

The parent gapmer, ISIS 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the selectivity of the modified oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 36, improvement in potency and selectivity was observed for chimeric oligonucleotides comprising 4-9-2 or 2-9-4 motif having the target SNP site at positions 3, 4, 6, 7 and 8 (ISIS540083, ISIS540084, ISIS 540085, ISIS 540094, ISIS 540096, ISIS 540097 and ISIS 540098) in comparison to position 8 of the parent gapmer (ISIS 460209). The remaining gapmers showed little to no improvement in potency or selectivity.

TABLE 35 Chimeric oligonucleotides designed by microwalk ISIS NO Sequence (5′ to 3′) SNP site Motif SEQ ID NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 8 3-9-3 10 (ekk-d9-kke) 543887 T_(e) T _(k) G_(k)T_(k)CATCACCAGA_(k)A_(e) 4 4-9-2 67 (ekkk-d9-ke) 540083 A_(e)A_(k)T_(k)T_(k)GTCATCACCA_(k)G_(e) 6 4-9-2 68 (ekkk-d9-ke) 540084 A_(e)A_(k)A_(k)T_(k)TGTCATCACC_(k)A_(e) 7 4-9-2 69 (ekkk-d9-ke) 540085 T_(e)A_(k)A_(k)A_(k)TTGTCATCAC_(k)C_(e) 8 4-9-2 10 (ekkk-d9-ke) 540087 A_(e)A_(k)T_(k)A_(k)AATTGTCATC_(k)A_(e) 10 4-9-2 70 (ekkk-d9-ke) 540090 A_(e)T_(k)T_(k)A_(k)ATAAATTGTC_(k)A_(e) 13 4-9-2 71 (ekkk-d9-ke) 540091 T_(e)A_(k)T_(k)T_(k)AATAAATTGT _(k) C_(e) 14 4-9-2 72 (ekkk-d9-ke) 540092 G_(e) T _(k) CATCACCAGA_(k)A_(k)A_(k)A_(e) 2 2-9-4 73 (ek-d9-kkke) 540093 T_(e)G_(k) TCATCACCAG_(k)A_(k)A_(k)A_(e) 3 2-9-4 74 (ek-d9-kkke) 540094 T_(e)T_(k)GTCATCACCA_(k)G_(k)A_(k)A_(e) 4 2-9-4 67 (ek-d9-kkke) 540096 A_(e)A_(k)TTGTCATCAC_(k)C_(k)A_(k)G_(e) 6 2-9-4 68 (ek-d9-kkke) 540097 A_(e)A_(k)ATTGTCATCA_(k)C_(k)C_(k)A_(e) 8 2-9-4 69 (ek-d9-kkke) 540098 T_(e)A_(k)AATTGTCATC_(k)A_(k)C_(k)C_(e) 8 2-9-4 10 (ek-d9-kkke) 540099 A_(e)T_(k)AAATTGTCAT_(k)C_(k)A_(k)C_(e) 9 2-9-4 75 (ek-d9-kkke) 540100 A_(e)A_(k)TAAATTGTCA_(k)T_(k)C_(k)A_(e) 10 2-9-4 70 (ek-d9-kkke) 540101 T_(e)A_(k)ATAAATTGTC_(k)A_(k)T_(k)C_(e) 11 2-9-4 76 (ek-d9-kkke) 540102 T_(e)T_(k)AATAAATTGT _(k) C_(k)A_(k)T_(e) 12 2-9-4 66 (ek-d9-kkke) e = 2′-MOE; k = cEt; d = 2′-deoxyribonucleoside

TABLE 36 Comparison of selectivity in HTT SNP inhibition of chimeric oligonucleotides with ISIS 460209 % UTC Selectivity SNP ISIS NO mut wt (wt vs. mut) site Motif 460209* 23 57 2.4 8 3-9-3 (ekk-d9-kke) 543887 18 43 2.3 4 4-9-2 (ekkk-d9-ke) 540083 18 67 3.7 6 4-9-2 (ekkk-d9-ke) 540084 10 49 4.9 7 4-9-2 (ekkk-d9-ke) 540085 21 86 4.1 8 4-9-2 (ekkk-d9-ke) 540087 60 98 1.6 10 4-9-2 (ekkk-d9-ke) 540090 129 137 1.1 13 4-9-2 (ekkk-d9-ke) 540091 93 105 1.1 14 4-9-2 (ekkk-d9-ke) 540092 28 55 2.0 2 2-9-4 (ek-d9-kkke) 540093 18 62 3.4 3 2-9-4 (ek-d9-kkke) 540094 13 45 3.4 4 2-9-4 (ek-d9-kkke) 540096 17 68 4.0 6 2-9-4 (ek-d9-kkke) 540097 8 35 4.2 8 2-9-4 (ek-d9-kkke) 540098 12 45 3.9 8 2-9-4 (ek-d9-kkke) 540099 62 91 1.5 9 2-9-4 (ek-d9-kkke) 540100 80 106 1.3 10 2-9-4 (ek-d9-kkke) 540101 154 152 1.0 11 2-9-4 (ek-d9-kkke) 540102 102 106 1.0 12 2-9-4 (ek-d9-kkke) e = 2′-MOE; k = cEt; d = 2′-deoxyribonucleoside

Example 14

Selectivity in Inhibition of HTT mRNA Levels Targeting SNP by Chimeric Oligonucleotides Designed by Microwalk

A series of modified oligonucleotides were designed based on the parent gapmer, ISIS 460209, wherein the central gap region comprises nine 2′-deoxyribonucleosides. These gapmers were created with various motifs and modifications at the wings and/or the central gap region.

The modified oligonucleotides and their motifs are described in Table 37. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e”, “k”, “y”, or “z” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt), a subscript “y” indicates an α-L-LNA modified nucleoside, and a subscript “z” indicates a F-HNA modified nucleoside. ^(P)U indicates a 5-propyne uridine nucleoside and ^(x)T indicates a 2-thio-thymidine nucleoside. Underlined nucleosides indicate the mismatch position.

These gapmers were evaluated for thermal stability (T_(m)) using methods described in Example 3. Presented in Table 38 are the T_(m) measurements for chimeric antisense oligonucleotides when duplexed to mutant or wild-type RNA complement. The T_(m) of chimeric antisense oligonucleotides duplexed with mutant RNA complement is denoted as “T_(m) (° C.) mut”. The T_(m) of chimeric antisense oligonucleotides duplexed with wild-type RNA complement is denoted as “T_(m) (° C.) wt”.

These gapmers were also tested in vitro. ISIS 141923 was included in the study as a negative control and is denoted as “neg control”. The non-allele specific antisense oligonucleotides, ISIS 387916 was used as a positive control and is denoted as “pos control”. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN. ISIS 460209 marked with an asterisk (*) in the table was included in the study for comparison. The results in Table 38 are presented as percent of HTT mRNA expression, relative to untreated control levels and is denoted as “% UTC”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT mRNA levels vs. the percent of mutant HTT mRNA levels.

As illustrated, several of the newly designed antisense oligonucleotides showed improvement in potency and/or selectivity in inhibiting mut HTT mRNA levels comparing to ISIS 460209.

TABLE 37 Modified oligonucleotides comprising various modifications targeting HTT SNP SEQ Wing Chemistry ID ISIS NO Sequence (5′ to 3′) Modification 5′ 3′ NO. 460209* T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 (ekk-d9-kke) 539560 T_(e)A_(k)A_(k)ATTG^(p)UCATCA_(k)C_(k)C_(e) 5-propyne in gap ekk kke 11 539563 T_(e)A_(k)A_(k)ATTG^(x)TCATCA_(k)C_(k)C_(e) 2-thio in gap ekk kke 10 539554 T_(e)A_(k)A_(k)ATTGU_(y)CATCA_(k)C_(k)C_(e) α-L-LNA in gap ekk kke 11 542686 T_(e)A_(k)A_(k)ATTGT_(z)CATCA_(k)C_(k)C_(e) F-HNA in gap ekk kke 10 540108 A_(e)T_(e)A_(e)A_(k)A_(k)TTGTCATC_(k)A_(k)C_(e)C_(e)A_(e) 5-7-5 eeekk kkeee 23 (eeekk-d7-kkeee) 544840 T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e)T_(k)T_(k)A_(k) 3-9-6 ekk kkekkk 15 (ekk-d9-kkekkk) 550904 T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e)T_(k)T_(k)T_(k)A_(k) 3-9-7 ekk kkekkkk 18 (ekk-d9-kkekkkk) 540082 A_(e)T_(k)T_(k)G_(k)TCATCACCAG_(k)A_(e) 4-9-2 ekkk ke 65 (ekkk-d9-ke) 540089 T_(e)T_(k)A_(k)A_(k)TAAATTGTCA_(k)T_(e) 4-9-2 ekkk ke 66 (ekkk-d9-ke) 540095 A_(e)T_(k)TGTCATCACC_(k)A_(k)G_(k)A_(e) 2-9-4 ek kkke 67 (ek-d9-kkke) 543528 A_(e)T_(k)A_(e)A_(k)AATGTCATCA_(k)C_(e)C_(k)A_(e) Mismatch at ekek keke 77 position 2 counting from 5′ gap 543533 T_(e)A_(k)A_(k)ATAGTCATCA_(k)C_(k)C_(e) Mismatch at ekk kke 78 position 3 counting from 5′ gap 387916 T_(e)C_(e)T_(e)C_(e)T_(e)ATTGCACATTC_(e)C_(e)A_(e)A_(e)G_(e) 5-10-5 eeeee eeeee 56 (pos control) 141923 C_(e)C_(e)T_(e)T_(e)C_(e)CCTGAAGGTTC_(e)C_(e)T_(e)C_(e)C_(e) 5-10-5 eeeee eeeee 57 (neg control) e = 2′-MOE; k = cEt; d = 2′-deoxyribonucleoside

TABLE 38 Comparison of selectivity in inhibition of HTT mRNA levels, and Tm of modified oligonucleotides with ISIS 460209 targeted to rs7685686 in GM04022 cells Tm (° C.) % UTC Selectivity Wing Chemistry ISIS NO mutant wt mut wt (wt vs mut) Modification 5′ 3′  460209* 53.7 52.2 23 57 2.7 3-9-3 ekk kke (ekk-d9-kke) 539560 54.1 50.8 13 32 2.4 5-propyne in gap ekk kke 539563 53.8 49.1 13 40 3.2 2-thio in gap ekk kke 539554 56.5 54.5 54 89 1.7 α-L-LNA in gap ekk kke 542686 56.1 50.4 26 62 2.4 F-HNA in gap ekk kke 540108 60.0 57.9 27 63 2.3 5-7-5 eeekk kkeee (eeekk-d7-kkeee) 544840 — — 19 40 2.1 3-9-6 ekk kkekkk (ekk-d9-kkekkk) 550904 — — 39 65 1.7 3-9-7 ekk kkekkkk (ekk-d9-kkekkkk) 540082 — — 21 62 3.0 4-9-2 ekkk ke (ekkk-d9-ke) 540089 — — 78 86 1.1 4-9-2 ekkk ke (ekkk-d9-ke) 540095 — — 22 66 3.1 2-9-4 ek kkke (ek-d9-kkke) 543528 50.5 49.1 44 90 2.1 Mismatch at ekek keke position 2 counting from 5′ gap 543533 47.0 44.8 83 97 1.2 Mismatch at ekk kke position 3 counting from 5′ gap 387916 — — 21 19 0.9 5-10-5 eeeee eeeee (pos control) 141923 — — 95 99 1.0 5-10-5 eeeee eeeee (neg control) e = 2′-MOE; k = cEt; d = 2′-deoxyribonucleoside

Example 15 Chimeric Oligonucleotides Comprising Modifications at the SNP Site of HTT Gene

Additional gapmers are designed based on the gapmer selected from studies described in Tables 73 and 74 (ISIS 540108) and is marked with an asterisk (*). These gapmers are designed by introducing modifications at the SNP site at position 9 of the oligonucleotides, as counted from the 5′-terminus and are created with a 5-7-5 motif.

The gapmers are described in Table 39. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “a”, “b”, “e”, or “k” are sugar modified nucleosides. A subscript “a” indicates 2′-(ara)-F modified nucleoside, a subscript “b” indicates a 5′-Me DNA modified nucleoside, a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(x)T indicates a 2-thio-thymidine nucleoside. Underline nucleoside or the number in parentheses indicates the position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus.

TABLE 39 Modified oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ID ISIS NO Sequence (5′ to 3′) Chemistry 5′ 3′ NO. 540108* (9) A_(e)T_(e)A_(e)A_(k)A_(k)TTGTCATC_(k)A_(k)C_(e)C_(e)A_(e) Deoxy eeekk kkeee 32 XXXX28 (9) A_(e)T_(e)A_(e)A_(k)A_(k)TTG ^(x) TCATC_(k)A_(k)C_(e)C_(e)A_(e) Deoxy/2- eeekk kkeee 32 thio XXXX29 (9) A_(e)T_(e)A_(e)A_(k)A_(k)TTGT _(a) CATC_(k)A_(k)C_(e)C_(e)A_(e) Deoxy/2′- eeekk kkeee 32 (ara)-F XXXX30 (9) A_(e)T_(e)A_(e)A_(k)A_(k)TTGT _(b) CATC_(k)A_(k)C_(e)C_(e)A_(e) Deoxy/5′- eeekk kkeee 32 Me-DNA e = 2′-MOE, k = cEt

Example 16 Chimeric Oligonucleotides Comprising Modifications at the Wing Regions Targeting HTT SNP

Additional gapmers are designed based on the gapmer, ISIS 540107 selected from Example 11 and is marked with an asterisk (*). These gapmers are designed by introducing bicyclic modified nucleosides at the 3′ or 5′ terminus and are tested to evaluate if the addition of bicyclic modified nucleosides at the wing regions improves the activity and selectivity in inhibition of mutant HTT SNP.

The gapmers comprise a 5-7-5 motif and are described in Table 40. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e”, or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

TABLE 40 Modified oligonucleotides targeting HTT SNP wing chemistry ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ SEQ ID NO. 540107* A_(e)T_(e)A_(e)A_(e)A_(k)TTGTCATC_(k)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeeek keeee 32 (eeeek-d7-keeee) XXXX31 A_(e)T_(e)A_(k)A_(k)A_(k)TTGTCATC_(k)A_(k)C_(k)C_(e)A_(e) 5-7-5 eekkk kkkee 32 (eekkk-d7-kkkee) XXXX32 A_(e)T_(e)A_(e)A_(e)A_(k)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeeek eeeee 32 (eeeek-d7-eeeee) XXXX33 A_(e)T_(e)A_(e)A_(k)A_(k)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeekk eeeee 32 (eeekk-d7-eeeee) XXXX34 A_(e)T_(e)A_(k)A_(k)A_(k)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e) 5-7-5 eekkk eeeee 32 (eekkk-d7-eeeee) XXXX35 A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(k)A_(e)C_(e)C_(e)A_(e) 5-7-5 eeeee keeee 32 (eeeee-d7-keeee) XXXX36 A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(k)A_(k)C_(e)C_(e)A_(e) 5-7-5 eeeee kkeee 32 (eeeee-d7-kkeee) XXXX37 A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(k)A_(k)C_(k)C_(e)A_(e) 5-7-5 eeeee kkkee 32 (eeeee-d7-kkkee) e = 2′-MOE; k = cEt; d = 2′-deoxyribonucleoside

Example 17 Chimeric Oligonucleotides Comprising Wing and Central Gap Modifications Targeting HTT SNP

Additional gapmers are designed based on the parent gapmer, ISIS 460209, wherein the central gap region comprises nine 2′-deoxyribonucleosides and is marked with an asterisk (*) in the table. These gapmers were designed by introducing modifications at the wings or the central gap region and are created with a 3-9-3 motif.

The gapmers are described in Table 41. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e”, or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside, and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(P)T indicates a 5-propyne thymidine nucleoside. ^(P)C indicates a 5-propyne cytosine nucleoside. Underline nucleoside or the number in parentheses indicates the position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus.

TABLE 41 Modified oligonucleotides targeting HTT SNP wing chemistry SEQ ISIS NO Sequence (5′ to 3′) Modification 5′ 3′ ID NO 460209* (8) T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) Deoxy gap ekk kke 10 (3-9-3) 552103 (8) T_(e)A_(e)A_(e)ATTGTCATCA_(k)C_(k)C_(k) Deoxy gap eee kkk 10 (3-9-3) 552104 (8) T_(k)A_(k)A_(k)ATTGTCATCA_(e)C_(e)C_(e) Deoxy gap kkk eee 10 (3-9-3) 552105 (8) T_(e)A_(k)A_(k)ATTG ^(P) T ^(P) CATCA_(k)C_(k)C_(e) Deoxy/5- ekk kke 10 Propyne 552106 (8) T_(e)A_(k)A_(k)A ^(P) T ^(P) TG^(P)T^(P)CA^(P)T^(P)CA_(k)C_(k)C_(e) Deoxy/5- ekk kke 10 Propyne e = 2′-MOE; k = cEt

Example 18 Modified Oligonucleotides Comprising F-HNA Modification at the Central Gap or Wing Region Targeting HTT SNP

A series of modified oligonucleotides were designed based on ISIS 460209, wherein the central gap region contains nine 2′-deoxyribonucleosides. These modified oligonucleotides were designed by incorporating one or more F-HNA(s) modification within the central gap region or on the wing regions. The F-HNA containing oligonucleotides were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting rs7685686 while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 42. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). Nucleosides followed by a subscript “z” indicate F-HNA modified nucleosides. ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The gap-interrupted antisense oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 43.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

The parent gapmer, 460209 is marked with an asterisk (*) in the table and was included in the study as a benchmark oligonucleotide against which the activity and selectivity of antisense oligonucleotides targeting nucleotides overlapping the SNP position could be compared.

As illustrated in Table 43, oligonucleotides comprising F-HNA modification(s) showed improvement in selectivity while maintaining activity as compared to the parent gapmer, ISIS 460209.

TABLE 42 Gap-interrupted antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 566266 T_(e)A_(k)A_(k)A_(z)TTGT 3-9-3 or Deoxy/F- ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 4-8-3 HNA ekkz 566267 T_(e)A_(k)A_(k)AT_(z)TGT 3-9-3 or Deoxy/F- ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 5-7-3 HNA ekkdz 566268 T_(e)A_(k)A_(k)ATT_(z)GT 3-9-3 or Deoxy/F- ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 6-6-3 HNA ekkddz 566269 T_(e)A_(k)A_(k)ATTG_(z) T 3-9-3 or Deoxy/F- ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 7-5-3 HNA ekkdddz 567369 T_(e)A_(k)A_(k)A_(z)T_(z)TGT 3-9-3 or Deoxy/F- ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 5-7-3 HNA ekkzz e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside, z = F-HNA

TABLE 43 Comparison of inhibition of HTT mRNA levels and selectivity of gap-interrupted antisense oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing Chemistry ISIS NO Mut Wt (wt vs mut) Motif Gap chemistry 5′ 3′  460209* 0.28 3.1 11 3-9-3 Full deoxy ekk kke 566266 0.20 >10 >50 3-9-3 or Deoxy/F-HNA ekk or ekkz kke 4-8-3 566267 0.90 >9.9 >11 3-9-3 or Deoxy/F-HNA ekk or ekkdz kke 5-7-3 566268 1.0 >10 >10 3-9-3 or Deoxy/F-HNA ekk or ekkddz kke 6-6-3 566269 1.7 >10.2 >6 3-9-3 or Deoxy/F-HNA ekk or ekkdddz kke 7-5-3 567369 0.82 >9.8 >12 3-9-3 or Deoxy/F-HNA ekk or ekkzz kke 5-7-3 e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside, z = F-HNA

Example 19 Modified Oligonucleotides Comprising cEt Modification(s) at the Central Gap Region Targeting HTT SNP

A series of modified oligonucleotides were designed in the same manner as described in Example 18. These modified oligonucleotides were designed by replacing F-HNA(s) with cEt modification(s) in the central gap region while maintaining the wing configuration. The modified oligonucleotides were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting rs7685686 while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 44. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The gap-interrupted antisense oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented below.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 45, some of the newly designed antisense oligonucleotides (ISIS 575006, 575007, and 575008) showed improvement in potency and/or selectivity in inhibiting mut HTT mRNA levels comparing to ISIS 460209.

TABLE 44 Gap-interrupted antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 575006 T_(e)A_(k)A_(k)A_(k)TTGT 4-8-3 Full deoxy ekkk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 575007 T_(e)A_(k)A_(k)AT_(k)TGT 3-9-3 or Full deoxy or ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 5-7-3 Deoxy/cEt ekkdk 575133 T_(e)A_(k)A_(k)ATT_(k)GT 3-9-3 or Full deoxy or ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 6-6-3 Deoxy/cEt ekkddk 575134 T_(e)A_(k)A_(k)ATTG_(k) T 3-9-3 or Full deoxy or ekk or kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 7-5-3 Deoxy/cEt ekkdddk 575008 T_(e)A_(k)A_(k)A_(k)T_(k)TGT 5-7-3 Deoxy ekkkk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside

TABLE 45 Comparison of inhibition of HTT mRNA levels and selectivity of gap-interrupted antisense oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing Chemistry ISIS NO Mut Wt (wt vs mut) Motif Gap chemistry 5′ 3′  460209* 0.28 3.1 11 3-9-3 Full deoxy ekk kke 575006 0.27 3.8 14 4-8-3 Full deoxy ekkk kke 575007 0.67 >10.1 >15 3-9-3 or Full deoxy or ekk or ekkdk kke 5-7-3 Deoxy/cEt 575133 3.0 >9 >3 3-9-3 or Full deoxy or ekk or ekkddk kke 6-6-3 Deoxy/cEt 575134 2.6 >10.4 >4 3-9-3 or Full deoxy or ekk or ekkdddk kke 7-5-3 Deoxy/cEt 575008 0.18 >9.9 >55 5-7-3 Deoxy ekkkk kke e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside

Example 20 Modified Oligonucleotides Comprising F-HNA Modification at the 3′-End of Central Gap Region Targeting HTT SNP

A series of modified oligonucleotides were designed based on ISIS 460209, wherein the central gap region contains nine 2′-deoxyribonucleosides. These modified oligonucleotides were designed by incorporating one F-HNA modification at the 3′-end of the central gap region. The F-HNA containing oligonucleotides were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 46. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). Nucleosides followed by a subscript “z” indicate F-HNA modified nucleosides. ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 47.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 47, a couple of the newly designed antisense oligonucleotides (ISIS 575833 and 575834) showed improvement in selectivity while maintaining potency as compared to ISIS 460209. ISIS 575836 showed an increase in potency without improvement in selectivity while ISIS 575835 showed comparable selectivity without improvement in potency.

TABLE 46 Modified oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ ID NO. 460209* T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 575833 T_(e)A_(k)A_(k)ATTGT 3-9-3 or Deoxy/F- ekk kke or 10 ^(m)C_(z)AT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 3-5-7 HNA zdddkke 575834 T_(e)A_(k)A_(k)ATTGT 3-9-3 or Deoxy/F- ekk kke or 10 ^(m)CA_(z)T^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 3-6-6 HNA zddkke 575835 T_(e)A_(k)A_(k)ATTGT 3-9-3 or Deoxy/F- ekk kke or 10 ^(m)CAT_(z) ^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 3-7-5 HNA zdkke 575836 T_(e)A_(k)A_(k)ATTGT 3-9-3 or Deoxy/F- ekk kke or 10 ^(m)CAT^(m)C_(z)A_(k) ^(m)C_(k) ^(m)C_(e) 3-8-4 HNA zkke e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside, z = F-HNA

TABLE 47 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing Chemistry ISIS NO Mut Wt (wt vs mut) Motif Gap chemistry 5′ 3′  460209* 0.28 3.1 11 3-9-3 Full deoxy ekk kke 575833 0.22 4.2 19 3-9-3 or Deoxy/F-HNA ekk kke or zdddkke 3-5-7 575834 0.30 6.3 21 3-9-3 or Deoxy/F-HNA ekk kke or zddkke 3-6-6 575835 0.89 9.8 11 3-9-3 or Deoxy/F-HNA ekk kke or zdkke 3-7-5 575836 0.09 0.4 4.6 3-9-3 or Deoxy/F-HNA ekk kke or zkke 3-8-4 e = 2′-MOE, k = cEt, d = 2′-β-deoxyribonucleoside, z = F-HNA

Example 21 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on ISIS 460209 and ISIS 540094 wherein the central gap region contains nine 2′-deoxynucleosides. These gapmers were designed with the central gap region shortened by introducing cEt modifications to the wing regions, or interrupted by introducing cEt modifications at the 3′-end of the the central gap region. The modified oligonucleotides were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209 and 540094.

The gapmers and their motifs are described in Table 48. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are 13-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 4 or 8 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 49.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 49, the newly designed antisense oligonucleotides (ISIS 575003) showed improvement in selectivity while maintaining potency as compared to ISIS 460209.

TABLE 48 Short-gap antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ NO. 460209* T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 540094* T_(e)T_(k)GT ^(m)CAT^(m)CA 2-9-4 Full deoxy ek kkke 67 ^(m)C^(m)CA_(k)G_(k)A_(k)A_(e) 575003 T_(e)T_(k)GT ^(m)CAT^(m)CA 2-8-5 Full deoxy ek kkkke 67 ^(m)C^(m)C_(k)A_(k)G_(k)A_(k)A_(e) 575004 T_(e)T_(k)GT ^(m)CAT^(m)CA 2-9-4 or Full deoxy or ek kkke or 67 ^(m)C_(k) ^(m)CA_(k)G_(k)A_(k)A_(e) 2-7-6 Deoxy/cEt kdkkke 575005 T_(e)T_(k)GT ^(m)CAT^(m)CA 2-7-6 Full deoxy ek kkkkke 67 ^(m)C_(k) ^(m)C_(k)A_(k)G_(k)A_(k)A_(e) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 49 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing Chemistry ISIS NO Mut Wt (wt vs mut) Motif Gap chemistry 5′ 3′  460209* 0.34 3.3 9.7 3-9-3 Full deoxy ekk kke  540094* 0.17 2.4 14 2-9-4 Full deoxy ek kkke 575003 0.40 10 25 2-8-5 Full deoxy ek kkkke 575004 1.2 >9.6 >8 2-9-4 or Full deoxy or ek kkke or kdkkke 2-7-6 Deoxy/cEt 575005 >10 >100 >10 2-7-6 Full deoxy ek kkkkke e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 22 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on 15-mer, ISIS 460209 and 17-mer, ISIS 476333 wherein the central gap region contains nine 2′-deoxynucleosides. These gapmers were designed with the central gap region shortened at the 5′-end of the the central gap region. The gapmers were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the gapmers were evaluated and compared to ISIS 460209 and ISIS 476333.

The gapmers and their motifs are described in Table 50. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are 13-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 or 9 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 51.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 51, a couple of the newly designed antisense oligonucleotides (ISIS 571036 and 571037) showed improvement in potency and selectivity in inhibiting mut HTT mRNA levels as compared to ISIS 460209 and 476333.

TABLE 50 Short-gap antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ NO. 460209* T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 476333* A_(e)T_(k)A_(e)A_(k)ATTGT 4-9-4 Full deoxy ekek keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) 571036 A_(e)T_(k)A_(e)A_(k)A_(e)T_(k)TGT 6-7-4 Full deoxy ekekek keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) 571037 A_(e)T_(e)A_(e)A_(e)A_(k)T_(k)TGT 6-7-4 Full deoxy eeeekk keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) 571038 A_(e)T_(k)A_(e)A_(k)A_(e)T_(e)TGT 6-7-4 Full deoxy ekekee keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 51 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) Motif chemistry 5′ 3′  460209* 0.34 3.3 9.7 3-9-3 Full deoxy ekk kke  476333* 0.32 1.5 4.7 4-9-4 Full deoxy ekek keke 571036 0.17 >10.0 >59 6-7-4 Full deoxy ekekek keke 571037 0.11 >9.9 >90 6-7-4 Full deoxy eeeekk keke 571038 1.5 >10.5 >7 6-7-4 Full deoxy ekekee keke e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 23 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on 15-mer, ISIS 460209 wherein the central gap region contains nine 2′-deoxynucleosides. These gapmers were designed by having the central gap region shortened to seven 2′-deoxynucleosides. The gapmers were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the gapmers were evaluated and compared to ISIS 460209.

The gapmers and their motifs are described in Table 52. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are 13-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 or 9 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 53.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 53, each of the newly designed antisense oligonucleotides (ISIS 540108 and 571069) showed improvement in potency and/or selectivity in inhibiting mut HTT mRNA levels as compared to ISIS 460209.

TABLE 52 Short-gap antisense oligonucleotides targeting HTT SNP Wing SEQ Gap chemistry ID ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 540108 A_(e)T_(e)A_(e)A_(k)A_(k)TTGT 5-7-5 Full deoxy eeekk kkeee 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(e) ^(m)C_(e)A_(e) 571069 A_(e)T_(e)A_(e)A_(e)A_(k)T_(k)TGT 6-7-4 Full deoxy eeeekk kkee 32 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e)A_(e) 571173 A_(e)T_(e)A_(k)A_(k)ATTGT 4-7-6 Full deoxy eekk kkeeee 32 ^(m)CAT_(k) ^(m)C_(k)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 572773 T_(e)A_(e)A_(k)A_(k)TTGT 4-7-4 Full deoxy eekk kkee 10 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(e) ^(m)C_(e) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 53 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) Motif chemistry 5′ 3′ 460209 0.34 3.3 9.7 3-9-3 Full deoxy ekk kke 540108 0.20 >10 >50 5-7-5 Full deoxy eeekk kkeee 571069 0.29 >9.9 >34 6-7-4 Full deoxy eeeekk kkee 571173 1.0 >10 >10 4-7-6 Full deoxy eekk kkeeee 572773 0.71 >7.8 11 4-7-4 Full deoxy eekk kkee e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 24 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on 15-mer, ISIS 460209 and 17-mer, ISIS 540108 wherein the central gap region contains nine and seven 2′-deoxynucleosides, respectively. These gapmers were designed by introducing one or more cEt modification(s) at the 5′-end of the central gap region. The gapmers were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the gapmers were evaluated and compared to ISIS 460209 and ISIS 540108.

The gapmers and their motifs are described in Table 54. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are 13-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 or 9 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 55.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 55, most of the newly designed oligonucleotides showed improvement in selectivity while maintaining potency as compared to 460209.

TABLE 54 Short-gap antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 540108 A_(e)T_(e)A_(e)A_(k)A_(k)TTGT 5-7-5 Full deoxy eeekk kkeee 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(e) ^(m)C_(e)A_(e) 556872 A_(e)T_(e)A_(e)A_(e)A_(k)TTGT 5-7-5 Full deoxy eeeek eeeee 32 ^(m)CAT^(m)C_(e)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 556873 A_(e)T_(e)A_(e)A_(k)A_(k)TTGT 5-7-5 Full deoxy eeekk eeeee 32 ^(m)CAT^(m)C_(e)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 556874 A_(e)T_(e)A_(k)A_(k)A_(k)TTGT 5-7-5 Full deoxy eekkk eeeee 32 ^(m)CAT^(m)C_(e)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 568877 A_(e)T_(k)A_(k)A_(k)A_(k)TTGT 5-7-5 Full deoxy ekkkk eeeee 32 ^(m)CAT^(m)C_(e)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 568878 A_(k)T_(k)A_(k)A_(k)A_(k)TTGT 5-7-5 Full deoxy kkkkk eeeee 32 ^(m)CAT^(m)C_(e)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 55 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) Motif chemistry 5′ 3′ 460209 0.45 2.3 5.1 3-9-3 Full deoxy ekk kke 540108 0.25 9.5 38 5-7-5 Full deoxy eeekk kkeee 556872 1.0 9.9 9.9 5-7-5 Full deoxy eeeek eeeee 556873 0.67 3.4 5.1 5-7-5 Full deoxy eeekk eeeee 556874 0.38 1.9 5.0 5-7-5 Full deoxy eekkk eeeee 568877 0.44 6.2 14 5-7-5 Full deoxy ekkkk eeeee 568878 0.41 8.6 21 5-7-5 Full deoxy kkkkk eeeee e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 25 Short-Gap Chimeric Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed based on 15-mer, ISIS 460209 and 17-mer, ISIS 540108 wherein the central gap region contains nine and seven 2′-deoxynucleosides, respectively. These gapmers were designed by introducing one or more cEt modification(s) at the 3′-end of the central gap region. The gapmers were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting HTT SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the gapmers were evaluated and compared to ISIS 460209 and ISIS 540108.

The gapmers and their motifs are described in Table 56. The internucleoside linkages throughout each modified oligonucleotide are phosphorothioate linkages (P═S). Nucleosides without a subscript are 13-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicate 2′-O-methoxyethyl (MOE) modified nucleosides. Nucleosides followed by a subscript “k” indicate 6′-(S)—CH₃ bicyclic nucleosides (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 or 9 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 57.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 57, each of the newly designed oligonucleotides showed improvement in selective inhibition of mutant HTT mRNA levels compared to ISIS 460209. Comparable potency was observed for ISIS 568879 and 568880 while a slight loss in potency was observed for ISIS 556875, 556876 and 556877.

TABLE 56 Short-gap antisense oligonucleotides targeting HTT SNP Wing Gap chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Motif chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 540108 A_(e)T_(e)A_(e)A_(k)A_(k)TTGT 5-7-5 Full deoxy eeekk kkeee 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(e) ^(m)C_(e)A_(e) 556875 A_(e)T_(e)A_(e)A_(e)A_(e)TTGT 5-7-5 Full deoxy eeeee keeee 32 ^(m)CAT^(m)C_(k)A_(e) ^(m)C_(e) ^(m)C_(e)A_(e) 556876 A_(e)T_(e)A_(e)A_(e)A_(e)TTGT 5-7-5 Full deoxy eeeee kkeee 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(e) ^(m)C_(e)A_(e) 556877 A_(e)T_(e)A_(e)A_(e)A_(e)TTGT 5-7-5 Full deoxy eeeee kkkee 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(k) ^(m)C_(e)A_(e) 568879 A_(e)T_(e)A_(e)A_(e)A_(e)TTGT 5-7-5 Full deoxy eeeee kkkke 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(k) ^(m)C_(k)A_(e) 568880 A_(e)T_(e)A_(e)A_(e)A_(e)TTGT 5-7-5 Full deoxy eeeee kkkkk 32 ^(m)CAT^(m)C_(k)A_(k) ^(m)C_(k) ^(m)C_(k)A_(k) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 57 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) Motif chemistry 5′ 3′ 460209 0.45 2.3 5.1 3-9-3 Full deoxy ekk kke 540108 0.25 9.5 38 5-7-5 Full deoxy eeekk kkeee 556875 1.9 >9.5 >5 5-7-5 Full deoxy eeeee keeee 556876 0.99 >9.9 >10 5-7-5 Full deoxy eeeee kkeee 556877 1.0 >10 >10 5-7-5 Full deoxy eeeee kkkee 568879 0.44 >10.1 >23 5-7-5 Full deoxy eeeee kkkke 568880 0.59 >10 >17 5-7-5 Full deoxy eeeee kkkkk e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 26 Modified Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

A series of modified oligonucleotides were designed based on the parent gapmer, ISIS 460209 wherein the central gap region contains nine 2′-deoxyribonucleosides. These modified oligonucleotides were designed by introducing various chemical modifications in the central gap region and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to the parent gapmer, ISIS 460209.

The modified oligonucleotides were created with a 3-9-3 motif and are described in Table 58. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages, except for the internucleoside linkage having a subscript “p” which indicates a methyl phosphonate internucleoside linkage (—O—P(CH₃)(═O)—O—). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. ^(x)T indicates a 2-thio-thymidine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 59.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 59, improvement in selectivity with a slight decrease in potency was observed for the newly designed oligonucleotides as compared to ISIS 460209.

TABLE 58 Short-gap antisense oligonucleotides targeting HTT SNP Wing chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Gap chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)ATTGT Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 556845 T_(e)A_(k)A_(k)A^(x)TTGT Deoxy/2-Thio ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 556847 T_(e)A_(k)A_(k)A^(x)T^(x)TGT Deoxy/2-Thio ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 558257 T_(e)A_(k)A_(k)ATT_(p)GT Deoxy/Methyl ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C Phosphonate 571125 T_(e)A_(k)A_(k)A^(x)TT_(p)GT Deoxy/2-Thio/Methyl ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) Phosphonate e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 59 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) chemistry 5′ 3′ 460209 0.56 3.8 6.8 Full deoxy ekk kke 556845 0.98 >9.8 >10 Deoxy/2-Thio ekk kke 556847 1.3 >10.4 >8 Deoxy/2-Thio ekk kke 558257 1.7 >10.2 >6 Deoxy/Methyl ekk kke Phosphonate 571125 1.8 >10.8 >6 Deoxy/2- ekk kke Thio/Methyl Phosphonate e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 27 Modified Oligonucleotides Comprising Chemical Modifications in the Central Gap Region Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed in the same manner as the antisense oligonucleotides described in Example 26. These gapmers were designed by introducing various modifications in the central gap region and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to the parent gapmer, ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 60. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages, except for the internucleoside linkage having a subscript “p” which indicates a methyl phosphonate internucleoside linkage (—O—P(CH₃)(═O)—O—). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. ^(x)T indicates a 2-thio-thymidine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 61.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 61, some of the newly designed oligonucleotides showed improvement in selectivity while maintaining potency as compared to 460209.

TABLE 60 Short-gap antisense oligonucleotides targeting HTT SNP Wing chemistry ISIS NO. Sequence (5′ to 3′) Motif Gap chemistry 5′ 3′ SEQ ID NO. 460209 T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 551429 T_(e)A_(e)A_(e)A_(k)T_(k)TGT 5-7-3 Full deoxy eeekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 571122 T_(e)A_(e)A_(e)A_(k) ^(x)TTGT 4-8-3 Deoxy/2-Thio eeek kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 571123 T_(e)A_(e)A_(e)A_(k)T_(k)T_(p)GT 5-7-3 Deoxy/Methyl eeekk kke 10 ^(m)CAT_(m)CA_(k) ^(m)C_(k) ^(m)C_(e) Phosphonate 571124 T_(e)A_(e)A_(e)A_(k) ^(x)TT_(p)GT 4-8-3 Deoxy/2- eeek kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) Thio/Methyl Phosphonate 579854 T_(e)A_(e)A_(e)A_(k)TT_(p)GT 4-8-3 Deoxy/Methyl eeek kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) Phosphonate 566282 T_(e)A_(k)A_(k)A_(dx)T_(dx)T_(d)G_(d)T_(d) ^(m)C_(d) 3-9-3 Deoxy/Methyl ekk kke 10 A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) Phosphonate e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 61 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) Motif chemistry 5′ 3′ 460209 0.56 3.8 6.8 3-9-3 Full deoxy ekk kke 551429 0.50 >10 >20 5-7-3 Full deoxy eeekk kke 571122 1.8 >10.8 >6 4-8-3 Deoxy/2-Thio eeek kke 571123 0.96 >9.6 >10 5-7-3 Deoxy/Methyl eeekk kke Phosphonate 571124 2.3 >9.2 >4 4-8-3 Deoxy/2- eeek kke Thio/Methyl Phosphonate 579854 0.63 >10.1 >16 4-8-3 Deoxy/Methyl eeek kke Phosphonate 566282 0.51 6.3 12.4 3-9-3 Deoxy/Methyl ekk kke Phosphonate e = 2′-MOE, k = cEt

Example 28 Modified Oligonucleotides Comprising Chemical Modifications in the Central Gap Region Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

Additional chimeric antisense oligonucleotides were designed in the same manner as the antisense oligonucleotides described in Example 26. These gapmers were designed by introducing various modifications to the central gap region and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to the parent gapmer, ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 62. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages, except for the internucleoside linkage having a subscript “p” which indicates a methyl phosphonate internucleoside linkage (—O—P(CH₃)(═O)—O—). Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. ^(x)T indicates a 2-thio-thymidine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 or 9 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented in Table 63.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 63, all but one of the newly designed oligonucleotides showed improvement in selectivity while maintaining potency as compared to ISIS 460209.

TABLE 62 Short-gap antisense oligonucleotides targeting HTT SNP Wing chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Motif Gap chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)ATTGT 3-9-3 Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 476333 A_(e)T_(k)A_(e)A_(k)ATTGT 4-94 Full deoxy ekek keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) 571039 A_(e)T_(k)A_(e)A_(k)A^(x)TTGT 4-9-4 Deoxy/2-Thio ekek keke 32 ^(m)CAT^(m)CA_(k) _(m)C_(e) ^(m)C_(k)A_(e) 571171 A_(e)T_(k)A_(e)A_(k)ATT_(p)GT 4-9-4 Deoxy/Methyl ekek keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) Phosphonate 571041 A_(e)T_(k)A_(e)A_(k)A^(x)TT_(p)GT 4-9-4 Deoxy/2- ekek keke 32 ^(m)CAT^(m)CA_(k) ^(m)C_(e) ^(m)C_(k)A_(e) Thio/Methyl Phosphonate e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 63 Comparison of inhibition of HTT mRNA levels and selectivity of modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) chemistry 5′ 3′ 460209 0.56 3.8 6.8 Full deoxy ekk kke 476333 0.56 3.4 6.1 Full deoxy ekek keke 571039 0.34 >9.9 >29 Deoxy/2-Thio ekek keke 571171 0.54 >10.3 >19 Deoxy/Methyl ekek keke Phosphonate 571041 0.75 >9.8 >13 Deoxy/2- ekek keke Thio/Methyl Phosphonate e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 29

Selectivity in Inhibition of HTT mRNA Levels Targeting SNP by Gap-Interrupted Modified Oligonucleotides

Additional modified oligonucleotides were designed based on the parent gapmer, ISIS 460209 wherein the central gap region contains nine 2′-deoxyribonucleosides. These modified oligonucleotides were designed by introducing one or more modified nucleobase(s) in the central gap region and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting SNP while leaving the expression of the wild-type (wt) intact. The activity and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The modified oligonucleotides were created with a 3-9-3 motif and are described in Table 64. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). ^(m)C indicates a 5-methyl cytosine nucleoside. ^(x)T indicates a 2-thio-thymidine nucleoside. Underlined nucleoside indicates the position on the oligonucleotides opposite to the SNP position, which is position 8 as counted from the 5′-terminus.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN.

The IC₅₀ and selectivity were calculated using methods previously described in Example 2. The IC₅₀ at which each oligonucleotide inhibits the mutant HTT mRNA expression is denoted as ‘mut IC₅₀’. The IC₅₀ at which each oligonucleotide inhibits the wild-type HTT mRNA expression is denoted as ‘wt IC₅₀’. Selectivity was calculated by dividing the IC₅₀ for inhibition of the wild-type HTT versus the IC₅₀ for inhibiting expression of the mutant HTT mRNA.

As illustrated in Table 65, ISIS 556845 showed improvement in selectivity and potency as compared to ISIS 460209. ISIS 556847 showed improvement in selectivity with comparable potency while ISIS 556846 showed improvement in potency with comparable selectivity.

TABLE 64 Gap-interrupted modified oligonucleotides targeting HTT SNP Wing chemistry ISIS NO. Sequence (5′ to 3′) Gap chemistry 5′ 3′ SEQ ID NO. 460209 T_(e)A_(k)A_(k)ATTGT Full deoxy ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 556845 T_(e)A_(k)A_(k)A^(x)TTGT Deoxy/2-Thio ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 556846 T_(e)A_(k)A_(k)AT^(x)TGT Deoxy/2-Thio ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) 556847 T_(e)A_(k)A_(k)A^(x)T^(x)TGT Deoxy/2-Thio ekk kke 10 ^(m)CAT^(m)CA_(k) ^(m)C_(k) ^(m)C_(e) e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

TABLE 65 Comparison of inhibition of HTT mRNA levels and selectivity of gap-interrupted modified oligonucleotides with ISIS 460209 targeting HTT SNP Selectivity Wing ISIS IC₅₀ (μM) (wt vs Gap Chemistry NO Mut Wt mut) chemistry 5′ 3′ 460209 0.30 0.99 3.3 Full deoxy ekk kke 556845 0.13 10.01 >77 Deoxy/2-Thio ekk kke 556846 0.19 0.48 2.5 Deoxy/2-Thio ekk kke 556847 0.45 9.9 >22 Deoxy/2-Thio ekk kke e = 2′-MOE, k = cEt, d = 2′-deoxyribonucleoside

Example 30 Evaluation of Modified Oligonucleotides Targeting HTT SNP—In Vivo Study

Additional modified oligonucleotides were selected and tested for their effects on mutant and wild type HTT protein levels in vivo targeting various SNP sites as illustrated below.

The gapmers and their motifs are described in Table 66. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. All cytosine nucleobases throughout each gapmer are 5-methyl cytosines. Nucleosides without a subscript are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” or “k” are sugar modified nucleosides. A subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside and a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt).

The gapmer, ISIS 460209 was included in the study as a benchmark oligonucleotide against which the potency and selectivity of the modified oligonucleotides could be compared. A non-allele specific oligonucleotide, ISIS 387898, was used as a positive control.

Hu97/18 mice, the first murine model of HD that fully genetically recapitulates human HD were used in the study. They were generated in Hayden's lab by cross bred BACHD, YAC18 and Hdh (−/−) mice.

Hu97/18 mice were treated with, 300 μg of modified oligonucleotides by a single unilateral intracerebroventricular (ICV) bolus injection. This treatment group consisted of 4 animals/oligonucleotide. The control group received a 10 μl bolus injection of sterile PBS and consisted of 4 animals.

Animals were sacrificed at 4 weeks post-injection. The second most anterior 2 mm coronal slab for each brain hemisphere was collected using a 2 mm rodent brain matrix. The remaining portion of the brain was post-fixed in 4% paraformaldehyde, cryoprotected in 30% sucrose and sectioned into 25 μm coronal sections for immunohistochemical analysis.

The HTT protein levels were analyzed by high molecular weight western blot (modified from Invitrogen's NuPAGE Bis-Tris System Protocol). The tissue was homogenized in ice cold SDP lysis buffer. 40 μg of total protein lysate was resolved on 10% low-BIS acrylamide gels (200:1 acrylamide:BIS) with tris-glycine running buffer (25 mM Tris, 190 mM Glycince, 0.1% SDS) containing 10.7 mM β-mercaptoethanol added fresh. Gels were run at 90V for 40 min through the stack, then 190V for 2.5 h, or until the 75 kDa molecular weight marker band was at the bottom of the gel. Proteins were transferred to nitrocellulose at 24V for 2 h with NuPage transfer buffer (Invitrogen: 25 mM Bicine, 25 mM Bis-Tris, 1.025 mM EDTA, 5% MeOH, pH 7.2). Membranes were blocked with, 5% milk in PBS, and then blotted for HTT with MAB2166 (1:1000, millipore). Anti-calnexin (Sigma C4731) immunoblotting was used as loading control. Proteins were detected with IR dye 800CW goat anti-mouse (Rockland 610-131-007) and AlexaFluor 680 goat anti-rabbit (Molecular Probes A21076)-labeled secondary antibodies, and the LiCor Odyssey Infrared Imaging system.

The results in Table 67 are presented as the average percent of HTT protein levels for each treatment group, normalized to PBS-treated control and is denoted as “% UTC”. The percent of mutant HTT protein levels is denoted as “mut”. The percent of wild-type HTT protein levels is denoted as “wt”. Selectivity was also evaluated and measured by dividing the percent of wild-type HTT protein levels vs. the percent of the mutant HTT protein levels.

As illustrated in Table 67, treatment with the newly designed oligonucleotides, ISIS 476333 and 460085 showed improvement in potency and selectivity in inhibiting mutant HTT protein levels as compared to the parent gapmer, 460209. Comparable or a slight loss in potency and/or selectivity was observed for the remaining oligonucleotides.

TABLE 66 Modified oligonucleotides targeting HTT rs7685686, rs4690072 and rs363088 in Hu97/18 mice Wing Chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif 5′ 3′ ID NO. 387898 C_(e)T_(e)C_(e)G_(e)A_(e)CTAAAGCAGGA_(e)T_(e)T_(e)T_(e)C_(e) 5-10-5 e5 e5 79 460209 T_(e)A_(k)A_(k)ATTGTCATCA_(k)C_(k)C_(e) 3-9-3 ekk kke 10 435879 A_(e)A_(e)T_(e)A_(e)A_(e)ATTGTCATCA_(e)C_(e)C_(e)A_(e)G_(e) 5-9-5 e5 e5 80 476333 A_(e)T_(k)A_(e)A_(k)ATTGTCATCA_(k)C_(e)C_(k)A_(e) 4-9-4 ekek keke 32 435874 C_(e)A_(e)C_(e)A_(e)G_(e)TGCTACCCAA_(e)C_(e)C_(e)T_(e)T_(e) 5-9-5 e5 e5 81 435871 T_(e)C_(e)A_(e)C_(e)A_(e)GCTATCTTCT_(e)C_(e)A_(e)T_(e)C_(e) 5-9-5 e5 e5 82 460085 A_(e)T_(e)A_(e)A_(e)A_(e)TTGTCATC_(e)A_(e)C_(e)C_(e)A_(e) 5-7-5 e5 e5 32 e = 2′-MOE (e.g. e5 = eeeee), k = cEt

TABLE 67 Effects of modified oligonucleotides on mutant and wild type HTT protein levels in Hu97/18 mice Selectivity Dosage % UTC (wt vs ISIS NO SNP site (μg) mut wt mut) PBS — 300 100 100 1 387898 — 300 23.76 25.66 1 460209 rs7685686 300 18.16 48.99 2.7 435879 rs7685686 300 41.48 73.11 1.8 476333 rs7685686 300 6.35 22.05 3.5 460085 rs7685686 300 2.9 40.1 13.8 435874 rs4690072 300 44.18 76.63 1.7 435871 rs363088 300 33.07 89.30 2.7

Example 31

Evaluation of ISIS 435871 in Central Nervous System (CNS) Targeting HTT rs363088—In Vivo Study

A modified oligonucleotide from Example 29, ISIS 435871 was selected and tested for its effects on mutant and wild type HTT protein levels in the CNS in vivo targeting rs363088.

Hu97/18 mouse was treated with, 300 μg of ISIS 435871 by a single unilateral intracerebroventricular (ICV) bolus injection. The animal was sacrificed at 4 weeks post-injection. Regional CNS structures were then micro-dissected including bilateral samples from the most anterior portion of cortex (Cortex 1), an intermediate section of cortex (Cortex 2), the most posterior section of cortex (Cortex 3), the striatum, the hippocampus, the cerebellum, and a 1 cm section of spinal cord directly below the brain stem. Tissue was homogenized and assessed for mutant and wild-type HTT levels by Western blotting using the procedures as described in Example 30. The results are presented below. As no untreated or vehicle treated control is shown, HTT intensity of each allele is expressed as a ratio of calnexin loading control intensity. The ratio of the mutant HTT to the wt HTT in the treated animal was determined and is denoted as “wt/mut”. Having a ratio higher than 1 is indicative of allele-specific silencing.

As illustrated in Table 68, a single unilateral ICV bolus injection of the modified antisense oligonucleotide showed selective HTT silencing throughout the CNS except in the cerebellum, where the antisense oligonucleotide did not distribute evenly.

TABLE 68 Effects of ISIS 435871 on mutant and wild type HTT protein levels in CNS targeting rs363088 in Hu97/18 mice HTT intensity/ calnexin intensity Tissue wt mut wt/mut Cortex 1 0.032 0.014 2.29 Cortex 2 0.027 0.009 3 Cortex 3 0.023 0.007 3.29 Striatum 0.030 0.012 2.5 Hippocampus 0.016 0.006 2.67 Cerebellum 0.023 0.019 1.21 Spinal Cord 0.014 0.007 2

Example 32

Evaluation of Modified Oligonucleotides Targeting HTT rs7685686—In Vivo Study

Several modified oligonucleotides from Examples 43, 51, 52, 53 and 66 were selected and tested for their effects on mutant and wild type HTT protein levels in vivo targeting HTT rs7685686.

The gapmer, ISIS 460209 was included in the study as a benchmark oligonucleotide against which the potency and selectivity of the modified oligonucletides could be compared.

Hu97/18 mice were treated with, 300 μg of modified oligonucleotides by a single unilateral intracerebroventricular (ICV) bolus injection. This treatment group consisted of 4 animals/oligonucleotide. The control group received a 10 μl bolus injection of sterile PBS and consisted of 4 animals.

Animals were sacrificed at 4 weeks post-injection. The second most anterior 2 mm coronal slab for each brain hemisphere was collected using a 2 mm rodent brain matrix. The HTT protein levels were analyzed in the same manner as described in Example 30 and the results are presented below.

The results in Table 69 are presented as the average percent of HTT protein levels for each allele and treatment group, normalized to PBS-treated control and is denoted as “% UTC”. The percent of mutant HTT protein levels is denoted as “mut”. The percent of wild-type HTTprotein levels is denoted as “wt”.

As shown in Table 69, each of the newly designed oligonucleotides showed improvement in selective inhibition of mutant HTT protein levels as compared to ISIS 460209. ISIS 550913 and 540095 showed improvement in potency while the remaining modified oligonucleotides showed comparable or a slight decrease in potency as compared to the parent gapmer.

TABLE 69 Effects of modified oligonucleotides on mutant and wild type HTT protein levels targeting rs7685686 in Hu97/18 mice Wing SEQ ISIS % UTC chemistry Gap ID NO mut wt Motif 5′ 3′ chemistry NO PBS 100 100 — — — — — 460209 18.16 48.99 3-9-3 ekk kke Full deoxy 10 550913 9.31 34.26 5-9-5 kkekk kkekk Full deoxy 27 540095 12.75 106.05 2-9-4 ek kkke Full deoxy 65 551429 19.07 108.31 5-7-3 eeekk kke Full deoxy 10 540094 24.68 87.56 2-9-4 ek kkke Full deoxy 67 540096 24.89 98.26 2-9-4 ek kkke Full deoxy 68 540108 28.34 85.62 5-7-5 eeekk kkeee Full deoxy 23 e = 2′-MOE, k = cEt

Example 33

Evaluation of Modified Oligonucleotides Targeting HTT rs7685686—In Vivo Study

Several modified oligonucleotides selected from Examples 57, 58, 61 and 62 were tested and evaluated for their effects on mutant and wild type HTT protein levels in vivo targeting HTT rs7685686.

Hu97/18 mice were treated with, 300 μg of modified oligonucleotides by a single unilateral intracerebroventricular (ICV) bolus injection and the control group received a 10 μl bolus injection of sterile PBS. Each treatment group consisted of 4 animals.

Animals were sacrificed at 4 weeks post-injection. The second most anterior 2 mm coronal slab for each brain hemisphere was collected using a 2 mm rodent brain matrix. The HTT protein levels were analyzed in the same manner as described in Example 30. The in vivo study for ISIS 575008 and 571069 marked with an asterisk (*) was performed independently and the results are presented below.

The results in Table 70 are presented as the average percent of HTT protein levels for each allele and treatment group, normalized to PBS-treated control and is denoted as “% UTC”. The percent of mutant HTT protein levels is denoted as “mut”. The percent of wild-type HTT protein levels is denoted as “wt”.

As illustrated in Table 70, selective inhibition of mut HTT protein levels was achieved with the newly designed oligonucleotide treatment as compared to PBS treated control.

TABLE 70 Effects of modified oligonucleotides on mutant and wild type HTT protein levels targeting rs7685686 in Hu97/18 mice Wing SEQ ISIS % UTC chemistry Gap ID NO mut wt Motif 5′ 3′ chemistry NO PBS 100 100 — — — — — 575007 26.9 104.5 3-9-3 ekk kke Deoxy/cEt 10  575008* 21.7 105.9 5-7-3 ekkkk kke Deoxy/cEt or 10 full deoxy 566267 32.8 109.3 3-9-3 ekk kke Deoxy/F-HNA 10 571036 30.3 103.3 6-7-4 ekekek keke Full deoxy 32 571037 32.8 111.9 6-7-4 eeeekk keke Full deoxy 32  571069* 29.4 109.8 6-7-4 eeeekk kkee Full deoxy 32 e = 2′-MOE, k = cEt

Example 34

Evaluation of Modified Oligonucleotides Targeting HTT rs7685686—In Vivo Dose Response Study

ISIS 476333, 435871, 540108, 575007 and 551429 from previous examples were selected and evaluated at various doses for their effect on mutant and wild type HTT protein levels in vivo targeting HTT rs7685686.

Hu97/18 mice were treated with various doses of modified oligonucleotides as presented in Table 71 by a single unilateral intracerebroventricular (ICV) bolus injection. This treatment group consisted of 4 animals/oligonucleotide. The control group received a 10 μl bolus injection of sterile PBS and consisted of 4 animals.

Animals were sacrificed at 4 weeks post-injection. The second most anterior 2 mm coronal slab for each brain hemisphere was collected using a 2 mm rodent brain matrix. The HTT protein levels were analyzed in the same manner as described in Example 30. The dose response study was performed independently for each modified oligonucleotide and the results are presented below.

The results in Table 71 are presented as the average percent of HTT protein levels for each allele and treatment group, normalized to PBS-treated control and is denoted as “% UTC”. The percent of mutant HTT protein levels is denoted as “mut”. The percent of wild-type HTT protein levels is denoted as “wt”.

As illustrated in Table 71, selective inhibition of mut HTT protein levels was achieved in a dose-dependent manner for the newly designed oligonucleotides.

TABLE 71 Dose-dependent effect of modified oligonucleotides on mutant and wild type HTT protein levels targeting rs7685686 in Hu97/18 mice Dosage % UTC SEQ ID ISIS NO (μg) mut wt Motif NO. PBS 0 100 100 — 476333 50 48.7 115 4-9-4 32 150 23.1 53.3 (ekek-d9-keke) 300 8.8 36.7 435871 75 114 118 5-9-5 82 150 47.3 80.3 (e5-d9-e5) 300 33 89.3 500 36 97.5 540108 75 30.5 71.7 5-7-5 32 150 22 81 (eeekk-d7-kkeee) 300 8.6 59.6 575007 150 41.5 110.7 3-9-3 10 300 29 119.4 (ekk-d-k-d7-kke) (deoxy gap interrupted with cEt) 551429 75 58 101.3 5-7-3 10 150 36.2 110.4 (eeekk-d7-kke) 300 19.7 107.8 e = 2′-MOE (e.g. e5 = eeeee), k = cEt, d = 2′-deoxyribonucleoside

Example 35 Modified Oligonucleotides Targeting Huntingtin (HTT) Single Nucleotide Polymorphism (SNP)

A series of modified oligonucleotides was designed based on a parent gapmer, ISIS 460209, wherein the central gap region contains nine β-D-2′-deoxyribonucleosides. The modified oligonucleotides were designed by introducing a 5′-(R)-Me DNA modification within the central gap region. The 5′-(R)-Me DNA containing oligonucleotides were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting rs7685686 while leaving the expression of the wild-type (wt) intact. The potency and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus is position 8.

The modified oligonucleotides were created with a 3-9-3 motif and are described in Table 72. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. Nucleosides followed by a subscript “d” are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Nucleosides followed by a subscript “z” indicates a 5′-(R)-Me DNA. “^(m)C” indicates a 5-methyl cytosine nucleoside.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with a single dose at 2 μM concentration of the modified oligonucleotide. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN.

The IC₅₀s and selectivities as expressed in “fold” were measured and calculated using methods described previously in Example 2. As illustrated in Table 73, treatment with the newly designed oligonucleotides showed comparable or a slight increase in potency and/or selectivity as compared to ISIS 460209.

TABLE 72 Gap-interrupted oligonucleotides comprising 5′-(R)-Me DNA targeting HTT SNP Wing chemistry SEQ ID ISIS NO. Sequence (5′ to 3′) Gap chemistry 5′ 3′ NO. 460209 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) Full deoxy ekk kke 10 556848 T_(e)A_(k)A_(k)A_(z)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) Deoxy/5′-(R)-Me DNA ekk kke 10 556849 T_(e)A_(k)A_(k)A_(d)T_(z)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) Deoxy/5′-(R)-Me DNA ekk kke 10 556850 T_(e)A_(k)A_(k)A_(d)T_(d)T_(z)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) Deoxy/5′-(R)-Me DNA ekk kke 10 e = 2′-MOE, k = cEt

TABLE 73 Comparison of inhibition of HTT mRNA levels and selectivity of gap- interrupted oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing chemistry ISIS NO. Mut Wt (wt vs mut) Gap chemistry 5′ 3′ 460209 0.30 0.99 3.3 Full deoxy ekk kke 556848 0.15 0.6 4.0 Deoxy/5′-(R)-Me DNA ekk kke 556849 0.16 0.46 2.9 Deoxy/5′-(R)-Me DNA ekk kke 556850 0.33 0.96 2.9 Deoxy/5′-(R)-Me DNA ekk kke e = 2′-MOE, k = cEt

Example 36 Modified Oligonucleotides Comprising 5′-(R)- or 5′-(S)-Me DNA Modification Targeting HTT SNP

A series of modified oligonucleotides was designed based on a parent gapmer, ISIS 460209, wherein the central gap region contains nine β-D-2′-deoxyribonucleosides. The modified oligonucleotides were designed by introducing 5′-(S)- or 5′-(R)-Me DNA modification slightly upstream or downstream (i.e. “microwalk”) within the central gap region. The gapmers were created with a 3-9-3 motif and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression. The potency and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus is position 8.

The modified oligonucleotides and their motifs are described in Table 74. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. Nucleosides followed by a subscript “d” are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Nucleosides followed by a subscript “v” indicates a 5′-(S)-Me DNA. Nucleosides followed by a subscript “z” indicates a 5′-(R)-Me DNA. “^(m)C” indicates a 5-methyl cytosine nucleoside.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used. Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.1, 0.4, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 uL 2×PCR buffer, 101 uL primers (300 uM from ABI), 1000 uL water and 40.4 uL RT MIX. To each well was added 15 uL of this mixture and 5 uL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN and the results are presented below.

The IC₅₀s and selectivities as expressed in “fold” were measured and calculated using methods described previously in Example 2. The results in Table 75 demonstrated that each of the newly designed oligonucleotides comprising 5′-(S)- or 5′-(R)-Me DNA within the central gap region achieved improvement in potency and selectivity as compared to the parent gapmer, ISIS 460209.

TABLE 74 Gap-interrupted oligonucleotides comprising 5′-(S)- or 5′-(R)-Me DNA targeting HTT SNP Wing Gap Chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif Chemistry 5′ 3′ ID NO 460209 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Full deoxy ekk kke 10 589429 T_(e)A_(k)A_(k)A_(d)T_(v)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 Me DNA 589430 T_(e)A_(k)A_(k)A_(d)T_(d)T_(v)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 Me DNA 589431 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(v) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 Me DNA 589432 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(v) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 Me DNA 594588 T_(e)A_(k)A_(k)A_(d)T_(v)T_(v)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 Me DNA 556848 T_(e)A_(k)A_(k)A_(z)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 556849 T_(e)A_(k)A_(k)A_(d)T_(z)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 556850 T_(e)A_(k)A_(k)A_(d)T_(d)T_(z)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 539558 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(z) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 594160 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(z)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 594161 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(z)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 589433 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(z) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 594162 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(z)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA 594589 T_(e)A_(k)A_(k)A_(d)T_(z)T_(z)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 Me DNA e = 2′-MOE; k = cEt

TABLE 75 Comparison of inhibition of HTT mRNA levels and selectivity of gap- interrupted oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Wing Chemistry ISIS NO. Mut Wt (wt vs. mut) Motif Gap Chemistry 5′ 3′ 460209 1.2 1.4 1.2 3-9-3 Full deoxy ekk kke 589429 0.22 3.3 15 3-9-3 Deoxy/5′-(S)-Me DNA ekk kke 589430 0.22 >10 >45.5 3-9-3 Deoxy/5′-(S)-Me DNA ekk kke 589431 0.16 1.9 11.9 3-9-3 Deoxy/5′-(S)-Me DNA ekk kke 589432 0.23 >10 >43.5 3-9-3 Deoxy/5′-(S)-Me DNA ekk kke 594588 0.81 >10 >12.3 3-9-3 Deoxy/5′-(S)-Me DNA ekk kke 556848 0.16 1.8 11.3 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 556849 0.14 1.1 7.9 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 556850 0.22 1.7 7.7 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 539558 0.38 3.8 10 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 594160 0.28 3.3 11.8 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 594161 0.28 >10 >35.7 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 589433 0.27 4.4 16.3 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 594162 0.27 3.5 13.0 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke 594589 0.48 4.4 9.2 3-9-3 Deoxy/5′-(R)-Me DNA ekk kke e = 2′-MOE; k = cEt

Example 37

Inhibition of HTT mRNA Levels Targeting SNP by Modified Oligonucleotides

Additional modified oligonucleotides were designed in a similar manner as the antisense oligonucleotides described in Example 36. Various chemical modifications were introduced slightly upstream or downstream (i.e. “microwalk”) within the central gap region. The gapmers were created with a 3-9-3 motif and were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression. The position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus is position 8. The potency and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The modified oligonucleotides and their motifs are described in Table 76. The internucleoside linkages throughout each gapmer are phosphorothioate (P═S) linkages. Nucleosides followed by a subscript “d” are β-D-2′-deoxyribonucleosides. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). Nucleosides followed by a subscript “b” indicates a 5′-(R)-allyl DNA. Nucleosides followed by a subscript “c” indicates a 5′-(S)-allyl DNA. Nucleosides followed by a subscript “g” indicates a 5′-(R)-hydroxyethyl DNA. Nucleosides followed by a subscript “i” indicates a 5′-(S)-hydroxyethyl DNA. “^(m)C” indicates a 5-methyl cytosine nucleoside.

The modified oligonucleotides were tested in vitro using heterozygous fibroblast GM04022 cell line. The transfection method and analysis of HTT mRNA levels adjusted according to total RNA content, as measured by RIBOGREEN were performed in the same manner as described in Example 37. The IC₅₀s and selectivities as expressed in “fold” were measured and calculated using methods described previously and the results are shown below. As presented in Table 77, several modified oligonucleotides achieved greater than 4.5 fold selectivity in inhibiting mutant HTT mRNA levels and, therefore, are more selective than ISIS 460209.

TABLE 76 Gap-interrupted oligonucleotides comprising 5′-substituted DNA targeting HTT SNP Wing ISIS Gap Chemistry Chemistry SEQ ID NO Sequence (5′ to 3′) Motif (mod position) 5′ 3′ NO 460209 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Full deoxy ekk kke 10 589414 T_(e)A_(k)A_(k)A_(d)T_(b)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 allyl DNA (pos 5) 589415 T_(e)A_(k)A_(k)A_(d)T_(d)T_(b)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 allyl DNA (pos 6) 589416 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(b) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 allyl DNA (pos 8) 589417 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(b) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 allyl DNA (pos 11) 589418 T_(e)A_(k)A_(k)A_(d)T_(c)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 allyl DNA (pos 5) 589419 T_(e)A_(k)A_(k)A_(d)T_(d)T_(c)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 allyl DNA (pos 6) 589420 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(c) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 allyl DNA (pos 8) 589421 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(c) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 allyl DNA (pos 11) 589422 T_(e)A_(k)A_(k)A_(d)T_(g)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 hydroxyethyl DNA (pos 5) 589423 T_(e)A_(k)A_(k)A_(d)T_(d)T_(g)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 hydroxyethyl DNA (pos 6) 589424 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(g) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 hydroxyethyl DNA (pos 8) 589437 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(g) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(R)- ekk kke 10 hydroxyethyl DNA (pos 11) 589426 T_(e)A_(k)A_(k)A_(d)T_(i)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 hydroxyethyl DNA (pos 5) 589427 T_(e)A_(k)A_(k)A_(d)T_(d)T_(i)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 hydroxyethyl DNA (pos 6) 589428 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(i) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 hydroxyethyl DNA (pos 8) 589425 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(i) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/5′-(S)- ekk kke 10 hydroxyethyl DNA (pos 11) e = 2′-MOE; k = cEt

TABLE 77 Comparison of inhibition of HTT mRNA levels and selectivity of gap- interrupted oligonucleotides with ISIS 460209 targeting HTT SNP IC₅₀ (μM) Selectivity Gap Chemistry Wing Chemistry ISIS NO Mut Wt (wt vs. mut) (mod position) Motif 5′ 3′ 460209 0.47 2.1 4.5 Full deoxy 3-9-3 ekk kke 589414 1.0 7.6 7.6 Deoxy/5′-(R)-Allyl DNA 3-9-3 ekk kke (pos 5) 589415 1.4 >10 >7.1 Deoxy/5′-(R)-Allyl DNA 3-9-3 ekk kke (pos 6) 589416 2.7 >10 >3.7 Deoxy/5′-(R)-Allyl DNA 3-9-3 ekk kke (pos 8) 589417 5.4 >10 >1.9 Deoxy/5′-(R)-Allyl DNA 3-9-3 ekk kke (pos 11) 589418 1.2 >10 >8.3 Deoxy/5′-(S)-Allyl DNA 3-9-3 ekk kke (pos 5) 589419 1.1 >10 >9.1 Deoxy/5′-(S)-Allyl DNA 3-9-3 ekk kke (pos 6) 589420 3.2 >10 >3.1 Deoxy/5′-(S)-Allyl DNA 3-9-3 ekk kke (pos 8) 589421 2.0 >10 >5.0 Deoxy/5′-(S)-Allyl DNA 3-9-3 ekk kke (pos 11) 589422 0.73 3.2 4.4 Deoxy/5′-(R)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 5) 589423 0.92 9.2 10 Deoxy/5′-(R)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 6) 589424 0.21 4.4 21 Deoxy/5′-(R)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 8) 589437 0.73 >10.2 >14 Deoxy/5′-(R)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 11) 589426 0.91 5.1 5.6 Deoxy/5′-(S)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 5) 589427 0.91 >10 >11 Deoxy/5′-(S)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 6) 589428 1.1 >11 >10 Deoxy/5′-(S)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 8) 589425 1.5 >10.5 >7 Deoxy/5′-(S)-Hydroxyethyl 3-9-3 ekk kke DNA (pos 11) e = 2′-MOE; k = cEt

Example 38 Modified Oligonucleotides Comprising Methyl Phosphonate Internucleoside Linkage Targeting HTT SNP—In Vitro Study

ISIS 558255 and 558256 from Example 10 were selected and evaluated for their effect on mutant and wild type HTT mRNA expression levels targeting rs7685686. ISIS 46020 was included in the study for comparison. The position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus is position 8.

Heterozygous fibroblast GM04022 cell line was used for the in vitro assay (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 μL 2×PCR buffer, 101 μL primers (300 μM from ABI), 1000 μL water and 40.4 μL RT MIX. To each well was added 15 μL of this mixture and 5 μL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN.

The IC₅₀s and selectivities as expressed in “fold” were measured and calculated using methods described previously in Example 2. As illustrated in Table 78, improvement in selectivity and potency was achieved with the modified oligonucleotides comprising methyl phosphonate internucleoside linkage as compared to ISIS 460209.

TABLE 78 Comparison of selectivity in inhition of HTT mRNA levels of antisense oligonucleotides with ISIS 460209 targeted to rs7685686 in GM4022 cells SEQ IC₅₀ (μM) Selectivity Wing Chemistry ID ISIS NO Mut Wt (wt vs mut) Motif Gap Chemistry 5′ 3′ NO 460209 0.30 0.99 3.3 3-9-3 Full deoxy ekk kke 10 558255 0.19 1.3 6.8 3-9-3 Deoxy/Methyl ekk kke 10 phosphonate 558256 0.20 1.3 6.5 3-9-3 Deoxy/Methyl ekk kke 10 phosphonate e = 2′-MOE (e.g. e5 = eeeee), k = cEt

Example 39 Modified Oligonucleotides Comprising Methyl Phosphonate or Phosphonoacetate Internucleoside Linkage(s) Targeting HTT SNP

A series of modified oligonucleotides were designed based on ISIS 460209 wherein the gap region contains nine β-D-2′-deoxyribonucleosides. The modified oligonucleotides were synthesized to include one or more methyl phosphonate or phosphonoacetate internucleoside linkage modifications within the gap region. The oligonucleotides with modified phosphorus containing backbone were tested for their ability to selectively inhibit mutant (mut) HTT mRNA expression levels targeting rs7685686 while leaving the expression of the wild-type (wt) intact. The potency and selectivity of the modified oligonucleotides were evaluated and compared to ISIS 460209.

The position on the oligonucleotides opposite to the SNP position, as counted from the 5′-terminus is position 8.

The modified oligonucleotides and their motifs are described in Table 79. Each internucleoside linkage is a phosphorothioate (P═S) except for the internucleoside linkage having a subscript “x” or “y”. Each nucleoside followed by a subscript “x” indicates a methyl phosphonate internucleoside linkage (—P(CH₃)(═O)—). Each nucleoside followed by a subscript “y” indicates a phosphonoacetate internucleoside linkage (—P(CH₂CO₂—)(═O)—). Nucleosides followed by a subscript “d” is a β-D-2′-deoxyribonucleoside. Nucleosides followed by a subscript “e” indicates a 2′-O-methoxyethyl (MOE) modified nucleoside. Nucleosides followed by a subscript “k” indicates a 6′-(S)—CH₃ bicyclic nucleoside (e.g. cEt). “^(m)C” indicates a 5-methyl cytosine modified nucleoside.

The modified oligonucleotides were tested in vitro. Heterozygous fibroblast GM04022 cell line was used (from Coriell Institute). Cultured GM04022 cells at a density of 25,000 cells per well were transfected using electroporation with, 0.12, 0.37, 1.1, 3.3 and 10 μM concentrations of modified oligonucleotides. After a treatment period of approximately 24 hours, cells were washed with DPBS buffer and lysed. RNA was extracted using Qiagen RNeasy purification and mRNA levels were measured by quantitative real-time PCR using ABI assay C_2229297_10 which measures at dbSNP rs362303. RT-PCR method in short; A mixture was made using 2020 μL 2×PCR buffer, 101 μL primers (300 μM from ABI), 1000 uL water and 40.4 μL RT MIX. To each well was added 15 μL of this mixture and 5 μL of purified RNA. The mutant and wild-type HTT mRNA levels were measured simultaneously by using two different fluorophores, FAM for mutant allele and VIC for wild-type allele. The HTT mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN.

The IC₅₀s and selectivities as expressed in “fold” were measured and calculated using methods described previously in Example 2. As illustrated in Table 80, most of the newly design oligonucleotides achieved improvement in selectivity while maintaining potency as compared to ISIS 460209.

TABLE 79 Modified oligonucleotides comprising methyl phosphonate or phosphonoacetate internucleoside linkage(s) targeting HTT SNP Wing Chemistry SEQ ISIS NO Sequence (5′ to 3′) Motif Gap Chemistry 5′ 3′ ID NO 460209 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Full deoxy ekk kke 10 566276 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(dx)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566277 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(dx) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566278 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(dx)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566279 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(dx)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566280 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(dx) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566283 T_(e)A_(k)A_(k)A_(d)T_(dx)T_(dx)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 573815 T_(e)A_(k)A_(k)A_(d)T_(dy)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573816 T_(e)A_(k)A_(k)A_(d)T_(d)T_(dy)G_(d)T_(d) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573817 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(dy) ^(m)C_(d)A_(d)T_(d) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573818 T_(e)A_(k)A_(k)A_(d)T_(d)T_(d)G_(d)T_(d) ^(m)C_(d)A_(d)T_(dy) ^(m)C_(d)A_(k) ^(m)C_(k) ^(m)C_(e) 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 e = 2′-MOE, k = cEt

TABLE 80 Comparison of selectivity in inhition of HTT mRNA levels of antisense oligonucleotides with ISIS 460209 targeted to rs7685686 in GM4022 cells SEQ Selectivity Wing Chemistry ID ISIS NO Mut IC₅₀ (μM)) (wt vs mut) Motif Gap Chemistry 5′ 3′ NO 460209 0.15 9.4 3-9-3 Full deoxy ekk kke 10 566276 0.76 12.8 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566277 0.20 17 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566278 0.25 8.9 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566279 0.38 — 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566280 0.27 47 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 566283 0.8 >100 3-9-3 Deoxy/Methyl phosphonate ekk kke 10 573815 0.16 18.8 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573816 0.55 18.1 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573817 0.17 22.5 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 573818 0.24 13.5 3-9-3 Deoxy/Phosphonoacetate ekk kke 10 e = 2′-MOE, k = cEt 

1.-272. (canceled)
 273. An oligomeric compound comprising a modified oligonucleotide consisting of 10 to 30 linked nucleosides, wherein the modified oligonucleotide has a modification motif comprising: a 5′-region consisting of 2-8 linked 5′-region nucleosides, each independently selected from among a modified nucleoside and an unmodified deoxynucleoside, provided that at least one 5′-region nucleoside is a modified nucleoside and wherein the 3′-most 5′-region nucleoside is a modified nucleoside; a 3′-region consisting of 3-8 linked 3′-region nucleosides, each independently selected from among a modified nucleoside and an unmodified deoxynucleoside, wherein the 3′-region comprises a BBA motif, wherein each A is a non-bicyclic modified nucleoside and each B is a bicyclic nucleoside, provided that the 5′-most 3′-region nucleoside is a modified nucleoside; and a central region between the 5′-region and the 3′-region consisting of 6-12 linked central region nucleosides, each independently selected from among: a modified nucleoside and an unmodified deoxynucleoside, wherein the 5′-most central region nucleoside is an unmodified deoxynucleoside and the 3′-most central region nucleoside is an unmodified deoxynucleoside; wherein the modified oligonucleotide has a nucleobase sequence complementary to the nucleobase sequence of a target region of a nucleic acid associated with a huntingtin transcript.
 274. The oligomeric compound of claim 273, wherein the nucleobase sequence of the target region of the target nucleic acid differs from the nucleobase sequence of at least one non-target nucleic acid by 1-3 differentiating nucleobases.
 275. The oligomeric compound of claim 274, wherein the target nucleic acid and the non-target nucleic acid are alleles of the huntingtin gene.
 276. The oligomeric compound of claim 275, wherein the single differentiating nucleobase is a single-nucleotide polymorphism.
 277. The oligomeric compound of claim 276, wherein the single-nucleotide polymorphism is selected from among: rs6446723, rs3856973, rs2285086, rs363092, rs916171, rs6844859, rs7691627, rs4690073, rs2024115, rs11731237, rs362296, rs10015979, rs7659144, rs363096, rs362273, rs16843804, rs362271, rs362275, rs3121419, rs362272, rs3775061, rs34315806, rs363099, rs2298967, rs363088, rs363064, rs363102, rs2798235, rs363080, rs363072, rs363125, rs362303, rs362310, rs10488840, rs362325, rs35892913, rs363102, rs363096, rs11731237, rs10015979, rs363080, rs2798235, rs1936032, rs2276881, rs363070, rs35892913, rs12502045, rs6446723, rs7685686, rs3733217, rs6844859, and rs362331.
 278. The oligomeric compound of claim 276, wherein the single-nucleotide polymorphism is selected from among: rs7685686, rs362303 rs4690072 and rs363088
 279. The oligomeric compound of claim 278, wherein the 3′-most 5′-region nucleoside comprises a bicyclic sugar moiety.
 280. The oligomeric compound of claim 279, wherein the bicyclic nucleoside is selected from among a cEt sugar moiety and an LNA sugar moiety.
 281. The oligomeric compound of claim 280, wherein the central region consists of 6-10 linked nucleosides.
 282. The oligomeric compound of claim 281, wherein the central region consists of 7 linked nucleosides.
 283. The oligomeric compound of claim 282, comprising at least one modified 5′-region nucleoside comprising a 2′-substituted sugar moiety.
 284. The oligomeric compound of claim 283, wherein at least one modified 5′-region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′ substituent selected from among: halogen, optionally substituted allyl, optionally substituted amino, azido, optionally substituted SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; optionally substituted O-alkylenyl-O-alkyl, optionally substituted alkynyl, optionally substituted alkaryl, optionally substituted aralkyl, optionally substituted O-alkaryl, optionally substituted O-aralkyl, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl; wherein each optionally substituted group is optionally substituted with a substituent group independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.
 285. The oligomeric compound of claim 283, wherein at least one modified 5′-region nucleoside comprises a 2′-substituted sugar moiety comprising a 2′-substituent selected from among: a halogen, OCH₃, OCH₂F, OCHF₂, OCF₃, OCH₂CH₃, O(CH₂)₂F, OCH₂CHF₂, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃ (MOE), O(CH₂)₂—SCH₃, O(CH₂)₂—OCF₃, O(CH₂)₃—N(R₁)(R₂), O(CH₂)₂—ON(R₁)(R₂), O(CH₂)₂—O(CH₂)₂—N(R₁)(R₂), OCH₂C(═O)—N(R₁)(R₂), OCH₂C(═O)—N(R₃)—(CH₂)₂—N(R₁)(R₂), and O(CH₂)₂—N(R₃)—C(═NR₄)[N(R₁)(R₂)]; wherein R₁, R₂, R₃ and R₄ are each, independently, H or C₁-C₆ alkyl.
 286. The oligomeric compound of claim 285, wherein the 2′-substituent is selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.
 287. The oligomeric compound of claim 283, comprising at least one modified 5′-region nucleoside comprising a 2′-MOE sugar moiety.
 288. The oligomeric compound of claim 287, comprising at least one modified 3′-region nucleoside comprising a bicyclic sugar moiety.
 289. The oligomeric compound of claim 288, comprising at least one modified 3′-region nucleoside comprising a cEt sugar moiety.
 290. The oligomeric compound of claim 289, comprising of at least one modified 3′-region nucleoside comprising a 2′-substituted sugar moiety.
 291. The oligomeric compound of claim 290, wherein the 2′-substituent is selected from among: a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—CH═CH₂, O(CH₂)₂—OCH₃, O(CH₂)₂—O(CH₂)₂—N(CH₃)₂, OCH₂C(═O)—N(H)CH₃, OCH₂C(═O)—N(H)—(CH₂)₂—N(CH₃)₂, and OCH₂—N(H)—C(═NH)NH₂.
 292. The oligomeric compound of claim 290, comprising at least one modified 3′-region nucleoside comprising a 2′-MOE sugar moiety. 